This is mostly a list of time saves and not a complete walkthrough; any corrections or additions to the strategies are greatly appreciated.

The most general tip to know is that tapping R raises your max running speed.
The only other glitch that works in every level is fall damage cancelling, but AFAIK it's only ever done it in practice, and it's either frame perfect or has a two frame window. To cancel your fall damage animation, saving 2 seconds, tap R + b on the frame before hitting the ground. Also, you can't pick up items while holding Y (run).

Though not a real manipulation of the game, sometimes I will flutter the directional button while holding Y to maintain a certain speed, which is usually just below Shaggy's running animation to time jumps. The improvements in acceleration and max speed that comes from R running only start when Shaggy has the run animation, and this is also when Shaggy will perform a high jump instead of a normal one.

The rest of the strategies are level specific, with the first level having the most glitches and the last level having the most softlocks you need to avoid. A lot of trouble can be caused with actor loading in the game. Sometimes it's mandatory to wait for Velma to appear somewhere, and sometimes it's just optimal to.

Stage 1: Red Ryan

-After showing Velma the suitcase and grabbing the trolley, when you go back to the first room in the level One-Eyed Matt will start a dialogue if you turn right. You can skip this dialogue by hitting him with the trolley before he gets a chance to speak.

Setup: Don't press any buttons when leaving the room with Velma, and at the sound of the last footstep from Shaggy hit right + A to throw the trolley. One-eyed Matt will appear, get hit, and Fred will tell you to keep moving. (From Prince_Leaf or HolySanctum, most likely)

-The vertical moving platform on the shipdeck can be avoided by placing the crate far right on the stack you're intended to drop it on, then high jump off the crate to above the cabin. Run across the roof and jump to the next platform, then tap R like mad for a leap of faith across the chasm.

If you do this correctly, you'll avoid landing on the second part of the ship deck and land high up on the next platform. Jump on the small tan platform and then to the crows nest looking platform, and finally R tap and jump to land high up on the right side of the screen. This avoids some damage, avoids waiting for all moving platforms, and can skip the final crate climb at the right side of the screen. It is the first difficult section in the game, however you lose only minimal time if you jump the chasm and land on the ship deck with a bonk while going to the teddy bear (about +2s).

When you head back from the teddy bear, line yourself up with the invisible wall on the right, then run left. Jump when you hear a double-step sound from Shaggy and aim for the star in line with the platform you jumped from just at the left edge of the play screen- there's an invisible platform you can land on that saves a fall damage animation.

Reverse your path back from the teddy from there. If done correctly there's only one damage animation- when you land across the chasm going back to the ship cabin. You sometimes can land on the higher platform, but this is slower as you have to decelerate to get down. A fall damage cancel would save another 2 seconds, but good luck getting one.

-A small time save can be managed by not picking up the trolley you threw at Matt until after completing the ship deck and getting the teddy bear. Because you have to wait for Velma after giving her the teddy bear, you don't have to run past the trolley while she's heading to the blue key door. This introduces some leniency in button input, and may save some time from not having to let go of run while passing the trolley earlier.

-If you wait for Velma in the room beyond the 'blue key' door, she will appear at the end of the level in the room near the gold bar.
Setup: Grab the trolley, open the blue key door, and wait with Shaggy inside the next door frame to minimize time between Velma appearing and Shaggy moving through the level. You can exit through the door before you see Velma, likely because she is just behind the door, ready to open it.

Timing for when you can proceed is probably fixed based on when you give Velma the teddy bear, and you can proceed about four to five seconds before you see Velma. This should be done carefully though as failing to load Velma before proceeding she will remain in the beginning half of the level and you will lose a lot of time backtracking to give her a clue later. The time elapsed between giving Velma the bear and proceeding should be about 36s, with some lag time included for going thru doors.

-Next is the first Sandwich minigame. These are the only RNG spots in the game, and they're a doozy. Oceanity originally did a bit of research and found a few rules to the game, which were later improved by CasperSFC: You need a stack of about 13 height on one hand, and for both stacks to be slightly taller than the fridge to trigger win condition. Scooby drops plate at 19 weight difference between both arms.

Food weight values:

Banana: 1 Tomato: 1 Pickles: 2 Salami: 2 Cheese: 4 Chicken: 4 Ham: 5

credits to Oceanity on the weight values. What a headache of a game.

-After the sandwich minigame is an early favorite: The soap skip. You can skip the next dialogue with One-Eyed Matt again by throwing the soap bar at him at the same time as his actor loads. Setup: Run full tilt into Daphne, she will tell you to clean the floor (seriously?). Run until you get to about where the grated floor is, then let go of run. Tap A just as you get to the barrel and you may throw the soap as the dialogue triggers. Careful: too late and you will lose time, as the soap will land behind him. If this happens, grab the soap and jump back as close to Daphne as possible before hitting One-Eyed Matt with it: this will save you the penalty of Daphne walking to Shaggy.

-You can shave time off of the hammer minigame by whacking your friends.

-Many people (Silent protagonist, Prince_Leaf, CasperSFC that I know of) independently found that you can walk through the TNT door before you see the second explosion animation, however the real time save was found by Casper. As Fred is centering into position at the door, attempt to walk through the door before you're ready. Your dialogue will overwrite Fred's- end your speech bubble as his begins then advance through the cutscenes as normal until after the two explosion animations play. Just before Fred plays his last speech bubble walk down through the door to skip being locked in place for ~+2s.

-A small time save can be gotten at the end of the level when you retrieve the gold bar from the submarine looking thing. When you exit the sub, jump twice. Shaggy was actually slightly too low on the level platform.
This saves Velma from walking down a few steps to meet you, and now you can talk to her directly upon her arrival in the room.

Stage 2: Carnival

• Jump over the Clown whenever he appears to avoid a damage animation.

• Not a time save, but if you jump over the first exit in the Spiral Slide minigame, you can collect full health from Scooby snacks and hit a secret second exit. Useful because Werewolfs are brutal in this stage.

• After the slide, make sure to show Velma the lantern or another clue (mallet and mop work) before the truck. If you fail to, Fred will not load at the big tent after the truck.

-Casper insisted on the viability of getting through the truck on an early cycle. As soon as you enter the truck while the black load screen is up, feather the right directional until you hear the drop audio cue for Shaggy hitting the truck floor. Immediately jump and land on the left corner of the first crate, jump again asap to the second higher crate's left corner, then R run and high jump to the first moving platform as it's going away. This sets up a pretty lenient run through the truck to the welding rod and back as the cycle hangs just slower than your sweep to the right. Head back left on the platforms and move up the three crates stacked in the center of the truck, jump left, then high jump right twice to begin traversing the final three stationary platforms to a moving vertical one.

• Prince_Leaf found a great backup line through the truck. Use your lantern to time your jumps to the moving platform. For example, try jumping to the first moving platform on the bottom of the 4th lantern flash, and on the bottom of the 12th flash, if you're all the way right after picking up the welding rod, run and jump left to grab the rightmost moving platform at ground level. If done correctly, it will be moving from left to right and will load on screen just as you jump. This is perhaps the earliest cycle possible through the truck: run and jump again to get to the stationary platforms, then do the same for the next moving platform.

Top section setup: After the three moving platforms in the bottom of the truck and after the three stacked crates, walk left on the first platform, then run and jump right. Jump and tap R ONLY in the air, and you should land on the first floating platform near the end of the truck. Jump across the floating platforms, grab the vertical moving one, and head towards the exit. Don't forget to grab the welding mask. (credits again to Prince_Leaf)

• If you delay very slightly after getting the trailer key from Velma, Fred will follow you through the level. This will save time when you talk to Velma with the clown costume, as he will show up earlier than if you didn't wait. This mostly adds some leniency to the gauntlet as you go to and from the last trailer.

-Even though the trap plan calls for a glue pot to trap the clown (green looking goop), the trap will work successfully without ever picking it up. You are intended to stick the clown to the X in the big top, but if you fire the cannonball without the clown stuck there it will instead hit the ground and trigger the end scene for the level. This skips a dangerous rat, running to pick up the glue, and running to the X to lay it down, with additional time loss avoided by not sticking Shaggy to the X for a few seconds (previously unavoidable). Of all the ways for this to be discovered, my brother remembered it from playing the game over a decade ago!

Stage 3: Swamp

• You can pick up the fan and generator as Fred puts them down to save a small amount of time.

-You can skip the tires altogether. Simply mash R to increase Shaggy's speed as he's running towards the chasm at the long branch and you can land on the lowest branch on the other side. If you go very quickly and are precise, you can catch the first cycle of the vertical platform, however more likely is that you just save the time needed to pick up the tires in the first place- call it a 10-20 second time save, depending on the cycle. (Prince_Leaf again!) Setup: While entering the screen for the jump, R run until the second step audio plays, then hold R until just before the third step audio and jump. Let go of run and the right directional, and if done correctly you should land just before the center of the lower branch with your momentum low enough to immediately turn around. Jump asap to the next branch, then turn and high jump towards the moving platform. If done correctly you will have enough height to clear the next highest platform. If you were fast you can immediately jump on the vertical platform, but if not you can jump to the highest branch, turn, and try again.

• Instead of taking the horizontal moving platform to the right over the bramble, land on the nest just before it and it will fall down to a branch below. R pump and jump right to skip the platformer, run to the right to where Velma is, then immediately backtrack and head down and right to the next section. This saves 2 seconds without fall damage cancelling (you can skip the nest), and could potentially save 4-5s with cancels.

-Feather your directions as you go into the actual swamp jumps to avoid going too quickly and dying in the pit.

• When you talk to Fred to set up the trap, have the fan ready, as it's what he wants first.

• Avoid touching the swamp monster when you kite him back to the trap on the first screen he appears at. If you do, BAM! softlock.

Stage 4: Spooky Mansion

Tapping R to run fast saves about 2-3 seconds at optimal speed due to their length!

• You can avoid a dialogue from Velma after getting the dye if you hit R shoulder to show her the dye before touching her sprite.

• When waiting for Velma to open the locked door, check the door before talking to her with the tuxedo. The dialogue is just slightly faster.

• Grab the yellow book and blue book from the library and do a clean run jump off of them to reach the attic area.

• Death warp back to the hallway with the yellow knight after getting the $5 plate.

• After getting the death warp, wait for Velma just outside of the door in the first hallway. If you attempt to flag her down, you may soft lock the end screen. (Altermentality strat)

• Head upstairs and collect the pole, then collect the rest of the trap items before talking to Fred (after showing Velma the plate), as you're already on the correct side of the hallways to do so

• Finally, make sure Velma is in her end position before going to kite Count Bagosi. Otherwise- BAM! softlock. (Altermentality strat)

There are other softlocks to avoid, but they're less touchy and aren't usually a problem. Good luck!