The Beginner Guide, Intermediate Route, Advanced Route, and Expert Route are all based on the “Caves Earliest” Route that visits Crystal Caves first and frees all of the kongs through their intended methods. If you have never run DK64 before, the Beginner Guide will be helpful as it removes all of the difficult glitches and explains the route in great detail. If you have any experience running DK64, starting with the Intermediate Route is standard. The Advanced Route is also available to see what the fastest methods are, and you may transition from the Intermediate to Advanced Route as you see fit. There are no phasewalks required in the Advanced Route. The Expert Route is the fastest route currently utilizing all of the tricks in the Advanced Route as well as phasewalks.

The Castle Kongs route is more difficult and is slower on Wii U Virtual Console, but not yet timed for the N64 version. The start of the run is completely different as the kongs are freed in Creepy Castle’s boss instead of through their intended methods. There are two different Castle Kongs routes included below. The route with phasewalks is currently the fastest known Castle Kongs route and includes many difficult glitches (but still slower than the Expert Route above). The N64 Japes for Moves route listed below is the route used in the fastest N64 101% speedrun currently.

While the VC Version is faster for 101%, the routes are still very similar between the two versions. The only major differences include several lag clips added into the N64 route. Gloomy Galleon is also slightly different between the two versions.

Links to 101% Routes (all routes are for the NTSC-U version unless specified):
101 Beginner Route
101 Intermediate Route
101 Advanced Route
101 Expert Route with Phasewalks
101 Castle Kongs Route with Phasewalks
101 Castle Kongs Route for N64 Japes for Moves
101 PAL Route Beginner Friendly
101 JPN Route Beginner Friendly

Tutorials:
Example Beginner Run by Connor75

Resources:
101 Dexdrive Savepack for N64
Saves are made using Znernicus’s 6:17 route. Still a good resource for ILs if you have access to a gameshark 3.0 or above and a dexdrive. Since it's based off an older route, the saves themselves are outdated, but still useful. Made by Kiwikiller67

101 Everdrive Savepack for N64
Saves are made for both Organic and Castle Kongs routes. Made by Zorulda.

101 Counter Program
Allows you to keep track of your 101% collectables. Developed by 2dos