plex0m4n: Many of Nifflas' Games can be done in one day like Knytt or Saira. The same applies for Daniel's Base games like Iji (which is already listed) or Hero Core. The free game Expendabros on Steam is also short (1-2h), but fun.
catpower1980 seems to disagree, at least with regards to Knytt Underground. :)
plex0m4n: Risk of rain is also a game that can be done in 1-1.5h , but I guess it falls in the same category as FTL and Rogue Legacy so it won't get listed.
Yes,
Risk Of Rain is more of a burst-play game that takes a number of rounds to truly complete, unless one is very good and very lucky the first few times. Two other games that I am currently playing which have short but incremental plays that improve your future condition are
Luftrausers and
Shattered Planet.