Basically every mobile and web game. Try mobile speedrunning! Here's one that hasn't been touched in 6 months: https://www.speedrun.com/Rocats
Upgrade Complete (https://www.speedrun.com/uc/) is a pretty fun webgame. Not terribly time consuming either.
Also, not quite "obscure" but Tetris for the Game Boy! It's a classic, can't go wrong with it.
Is that the game where it's basically a loading screen that says "LOADING...", but when the progress bar gets to the end, the game is over, like the loading screen progress bar ¤was¤ the game? I've heard there's something out there like that, but I've never seen it..
Stardew Valley isn't a small game, but very few people are running it. I would find it very cool if more people did Stardew Valley runs.
It would be really cool if more people ran The Adventures of Batman and Robin on the SNES. It's a nice 2D Platformer, with a really good soundtrack and some nice speedstrats. Also it's style is very close to the Animated Series, so that's a huge plus :)
I wish more than 2 people ran Perfect Dark Zero. Granted, as a casual game it's not very good, but as a speedgame it's oddly satisfying
Not sure if obscure enough but Momodora III is a nice game and it would be nice to get more runners.
I'm obviously a little bit biased but, I do recommend Alien Splatter Redux. It's only a dollar, and if your run is deathless, then your playthrough of the main game should only be about 20 minutes or so. It's kind of in the sweet spot for me in being long enough that there's interesting things to do and think about, but short enough that it didn't take me a month and change to develop a solid run.
I don't see 100% Orange Juice on here yet, so there ya go. Also GEAR. Seriously. I am the only person outside of this http://b-lee.net/gear/team team who has heard of this game which is already so old, if you try to do two runs without restarting, chances are it's going to crash on you after the first gold split.
How do you even speedrun 100% Orange Juice? The campaign? I don't think running multiplayer games would make sense
I wish more obscure RPGs were ran like Grandia, Lunar, and third person dark games like King's Field.
I'm a new runner, but I've been trying to get more people to speedrun Gunpoint. It's a fun, movement-based puzzle-platformer, where you play as a spy, and Any% runs go under ten minutes. It seems its popularity dropped off years ago.