My tastes change over time, so I don't use the term favorites, but I can say which games I keep going back to
1. The final fantasy series. Everyone who's played more than 1 game from this series has played most of them, so it's really a question of your preferred ordering. Mine is 7, 6, 5, 9, 3, etc. etc. And for what it's worth, I'll lump Chrono Trigger in with this one, since it's an FF game in spirit.
2. Actraiser. Remember that one where you play god bringing humanity back to earth by killing demons and then building their towns SimCity style? I really loved this one. I play it start-to-finish about once a year.
3. Minecraft. I've been too busy to play it much in the last few months, but this is a great game. Especially if you've got friends and family who will play SMP with you over a very long period. Actually, I have a flickr set from a long while ago where a friend, my younger brother, and I took on
Super Hostile: Legendary. That was an awesome map. Also here's a tour of my SMP server from 2012,
Slightly Burning.
4. I played Left4Dead and Left4Dead2 a _lot_. I'm not very big on shooters, but this was a great shooter. It really did get how a Co-Op game should work.
5. Portal and Portal 2 are also freaking great games. Valve really understands how to make something entertaining.
Honorable Mentions:
1. I played a lot of jRPGs when I was younger. I have a place in my heart for Wild Arms, Legend of Legaia, Disgaea (and La Pucelle and Phantom Brave).
2. The Metal Gear Solid series is a total mindbender.
3. I was big in the Megazeux community like 10 years ago. There's way too much stuff there to list.
4. There's been some pretty good indie games as of late. Bastion and Thomas Was Alone deserve highlighting.
So, thanks guys for letting me wallow in Nostalgia for a few minutes.