I've missed out on quite a few "greats", so here's my list:
1.) Final Fantasy 7
2.) Shining Force
3.) Uncharted Waters (especially 2)
4.) Romance of the Three Kingdoms (the whole darn series!)
5.) Dragon Age (1 AND 2!)
6.) Civilization (I never played the first, but I played the 2nd/3rd/4th/5th to DEATH, even moreso with mods)
7.) Final Fantasy Tactics (original PSX, never played the others)
8.) Star Ocean: Second Story
9.) Elder Scrolls (Morrowind especially, but Oblivion and Skyrim were top-notch too)
10.) PLANTS VS ZOMBIES! =) Best ending EVER.