Endless Sky – open-source space game. I actually contributed to it back in the day; a date format option and a full-blown storyline about an author. Unfortunately the storyline is in development hell cause I lost motivation to work on it.
OpenTTD – really awesome, with NewGRFs and mods you can have a somewhat “realistic” rail experience (as in, using actual real-life trains. Obviously a pixel game isn’t the most “realistic” with graphics)
Widelands is a great strategy / building game. The gameplay and UI style is a niche - but that’s one of the things I like about it. It’s doing something different to most games.
(The gameplay is similar to Settlers 2; before that franchise changed direction.)
[edit] But the open-source game I’ve spent the most time playing would be OpenXcom-extended, with xpiratez. That game is truly huge.
Apotris is an excellent famous-block-stacking-game clone for the GBA (and other platforms), it has a version for Portmaster that will run on many if not all Linux handhelds like the RG35XX and similar, but will also run in any GBA emulator.
Andor’s Trail - RPG where you search for your missing brother. Still under development, but there’s a lot of content. It’s convenient to fill a few spare minutes or waste hours.
It’s a time machine that teleports you to 3am the next day.
Sanmill
Basically nine man’s morris, it’s pretty fun trying to beat progressively harder AI. Each difficulty requires a different (better) strategy. It’s like unlocking levels in a puzzle game.