That may not be useful to a lot of other people as a recommendation, but No Thank You, Evil! and Hero Kids are both designed with shorter scenarios and challenges in mind, due to their target audience. I don't think I've ever run NTYE! for more than an hour at a time. Outside specific games, I'd probably focus on lean games with simpler character sheets, like Risus or Fate Accelerated. FAE + It's Not My Fault would work well.
But… I mean… Almost all my weekly Roll20 gaming is comprised of 2 to 2.5 hour sessions, so… pretty much any system, I guess, if you're talking about being able to play multiple short sessions.
ALSO, any game where everyone playing is on the hook to come up with a lot of stuff out of their head, all the time, is probably best confined to shorter sessions. I find people lose their inventive steam after a few hours, so if you want to keep things popping in games where the players have to invent a lot of stuff on the fly, I'd recommend shorter sessions.
NTYE, excellent entry. We got past the 90 minute mark once but it made my wife antsy. Kiddo was ready to rock until we all lost our voices.