I'll actually explain some of them.

Final Fantasy Game: FF6

A just like how the story is done, every character plays a part and their reasons for coming with you are explained well. Plus, it has Kefka.

Non-Final Fantasy Game: Suikoden 2

One of the most complex dark stories ever told. Plus, it's a neat combination of RPG and strategy game.

Character: Viktor (Suikoden 2)

He was just badass in general. Always drunk and walking around with a chip on his shoulder, yet still reliable and quite intelligent. Plus, he had a talking sword that he always argued with. Shame he didn't show up in part 3.

Side-Character: Lacan (Xenogears)
Villain: Grahf (Xenogears)

Reasons would be spoilers.

Boss: Jowy (Suikoden II)

Well, more for the same reasons I like Grahf. Jowy starts the game as your best friend, but slowly becomes an enemy. You are drawn into conflict with him even though he also believes he is helping the kingdom in his own way.

Enemy: Tonberry

The buggers can really be a pain in your side in some of the FFs.

Weapon: Lionheart (FF8)

I have to agree. Gunblades are just cool.

Town: Tie - Solaris (Xenogears)/Broken Hills (Fallout 2)
Dungeon:Vault 15 (sort of a dungeon)
FMV: The Highwind's transformation in FF7
Mini-Game: Tetra Master (FF9)


Least Favorites

Final Fantasy Game: FF8 (but I don't hate it)
Non-Final Fantasy Game: Silent Hill 2
Character: Cecil
Side-Character: Baigan (FF4)
Villain: Seifer (FF8)
Boss: Chameleon Man (Wild Arms 3. Oh joy, a boss who's every second move instant kills your entire party!)