Here's my favourites:
Blob wars is a 2d platform/shooter that is great fun (great sound effects and hilariously excessive gore).
Warzone 2100 is an RTS with a "neoclassic" appeal (something that would have felt like "the future of RTS" back when you played Command&Conquer).
Battle of Wesnoth is a hex-grid strategy games with loads of mods and campaigns.