Console games only, no PC or handhelds. My top 25:
Yes I know, a surprising first but damn I <3 goemon and the second game for N64 is amazing and very underrated. It also features an excellent 2 player co-op option.
1) Goemon's Great Adventure N64
2) Final Fantasy XII - int edition ps2
3) Chrono Trigger snes
4) Act Raiser 1 snes
5) Castlevania IV snes
6) Final Fantasy VIII ps1
7) Legend of the mystical Ninja aka Ganbare Goemon 1 snes
8.) Toejam and Earl 1 Megadrive
9) Final Fantasy VI snes
10) Castlevania SotN ps1
11) Resident Evil 4 gc
12) Tales of the Abyss ps2
13) Mega Man II nes
14) Illusion of Gaia snes
15) TMNT in time snes
16) Strider Megadrive
17) Mortal Kombat II snes
18) Goonies II nes
19) Zillion Master System
20) REmake gc
21) Faxandu nes
22) Wizards & Warriors 3 nes
23) rock n roll racing snes, megadrive
24) Secret of Mana snes
25) Killer7 gc, ps2