I would have a whole seperate top 10 just for RPGs.
In no particular order:
1: Xenogears
2: FF 3 (US), 7, 8, and the remakes of 2 & 3 for PSP, Tactics, and Lions. Oh, and the WiiWare one too.
3: Breath of Fire (pick any one, but loved the ps1 one! Still a great play, even if you opt for the psp remake, which was more or less a port anyways)
4: Any Dragon Warrior, but really loved the PS1 version that everyone hated... VII I think?
5: Super Mario RPG series, Paper Mario (Dream Team is awesome!)
6: Ultima series (I remember burning many hours on Exodus)
7: Any Zelda, my favorites being Wind Waker, Spirit Tracks, and the latest 3DS one (Link Between Worlds)
8: Suikoden (any of them but especially the first one on PS1)
9: Jeanne d'Arc (if you never got a chance to play this one, youre really missing out on something awesome)
10: Chrono Trigger (of course!)
And for the ones that probably should make the list:
Golden Sun (great series!), Star Ocean (any one, but really loved the 2 on PSP), Pokemon (when it wasn't cool yet, you know back when 50 shades of grey meant youre handheld's screen colors), Legend of Heroes (any of the 3 on PSP), Phantasy Star (IV being my favorite), and of course the Lunar series.
I could probably even do a top 50.