In no particular order
1. Final Fantasy VI
This game had charm, and lots of it. Gameplay wise it is probably where the series starts losing whatever dificulty it had but it is still a blast to play. I also find the sprites have passed the test of time better than certain early 3D games like FFVII and Legend of Dragoon. Not to mention you can suplex a train.
2. Suikoden II/V
I have actually played V more times than II. Story wise and music wise II is probably better but V kept drawing me back. I thought war battles were better done in V. I was not a huge fan of them in II.
3. The Elder Scrolls III: Morrowind
By far my favourite Elder Scrolls game. The world felt more alien than oblivion and Skyrim which really drew a player in. Exploring was really fun too. I actually liked the absence of a quest marker although some of the journal hints were confusing if not plain wrong. The combat is a bit difficult to get used to although if you can manage to get a skill past 45 you will be able to hit the vast majority of the time. The ashy voices of the Dunmer are also awesome.
4. Rune Factory 3
There was such a huge jump in quality from 2 to 3 that it was surprising. Frontier was great but 3 just seemed to have everything and more.
5. Crash Bandicoot 3/Spyro the Dragon
Yes, these are here. No, it is not a mistake.
6. Shadow of the Colossus
Great game. The satisfaction of finding out the weakness of a colossi was probably the best part of the game for me although some just click with you instantly
7. Trails in the Sky
This game just clicked with me. It is one of the few games where I spoke to every NPC repeatedly without regret. Each one seemed to have their own mini story going on rather than the usual "Welcome to town A" or "I have heard the villain is villainous"
8. Radiant Historia
I am a sucker when it comes to time travel games.
9. Thief 2: The Metal Age
I am not normally a big fan of stealth games but really enjoyed playing this game. The first game is also great.
10. Shin Megami Tensei III: Lucifer's Call
I really enjoyed the minimalistic story going on and the gameplay was also great.
Crash Team Racing (I prefer it to Mario Cart)
Tomba (Play it)
Tales of the Abyss (Only played it recently on 3DS but it jumped up to being my favourite tales game)
Xenoblade (My favourite game on the Wii...although it does not exactly have much competition
Breath of fire IV (I hated this game for years. It was just so different to the other titles but then something clicked making it my second favourite BoF game.
Valkyria Chronicles (This game was just great)
Disgaea: Afternoon of Darkness