Abuse
AisleRiot
Anagramarama
Armagetron Advanced
Battle for Wesnoth
BZFlag
DeSmuME
Emilia Pinball
FooBillard
Freeciv
FreeDink
FreeDoom
FrozenBubble
GNUbik
Gweled
LinCity
LTris
Mednafen
Micropolis
Minetest
NetHack
Neverball
Neverputt
Nexuiz
Pingus
PrBoom
Rocks'n'Diamonds
Secret Maryo Chronicles
SuperTux
The Mana World
Vectoroids
Yabause

Not confirmed if inside the Free Software Directory, or absent on it:
DOSBox
Dungeon Crawl Stone Soup
Egoboo
Enigma
Fish Fillets
Freedroid RPG
Frogatto and Friends
Gbrainy
Hedgewars
Mupen64
OpenTTD
PCSXR
Ryzom
StepMania
SuperTuxKart
Teeworlds
Warsow
Xonotic