I don't know if this makes any sense but my favorite game(s) of all time, Jak and Daxter, isn't the best game I've ever played. That crown would go to Persona 3/4. 

I guess it comes down to if I had to choose which game I would rather play for the rest of my life it would be Jak and Daxter even though I consider Persona a much better game.

So the question to you guys is simple, is your favorite game also the best game you've ever played or are youlike me where they are different?

Also the reason this popped into my head is because the Jak Collection just got rated by the ESRB  for the Vita and i'm EXTREMELY pump that I can play my favorite games on the go along with the best games I've ever played!

Yes.

My favorite game of all time is Wind Waker but I never finished it nor do I consider it the best game I've played.

The "Best game" I've played in terms of mechanics/value/replayability just everything in general is SSBM.

And yet I still enjoy WW more even though there are flaws in it.

Best game I've played is Ico.
Favorite game is Everquest.

One I played for daily for 4 years, the other 3 play-throughs totalling 20 hours.

How can you not finish your favorite game of all time?

Yeap...

My favorite series is Gran Turismo but I think the best game I ever played is a close battle between Ocarina of Time, Uncharted 2/3, BioShock, Portal, Half-Life 2, MGS4 and ICO.

Triforce fetch quest. It killed my 9 year old patience.

I see... it did test my patience also. Wind Waker ranks lower in my top Zelda games because of it actually. I sincerely hope they fix it for the remake.

Yes, but it's close. Final Fantasy Tactics is my favorite game of all time but I would probably rate Final Fantasy VI above it. They're both right at the top for either category, though.

Some recent games that I enjoyed at ton but would rate down a bit if I were giving an objective review would be Fallout 3/NV and Dragon Age: Origins/2. Loved all four games to death and played them all for many, many hours, but I'm fully aware that all of them are deeply flawed.

OoT is like the origin of all those games lol. Not my favorite zelda but definitely best game played (after SSBM of course :P)

My alltime no 1 is Wipeout 2097(xl)because it does something unique-simulating something in a perfect way that does not exist in reality(as long as you use a negcon)
but the best game i've ever played is zelda oot

I think this is not unusual to differ between best and favourite,as Wipeout is a racing game and therefore repetitiv ,there is no such thing like storytelling etc,but a lot adrenalin.
Zelda oot gives you tons of more variety and a great atmosphere and it was new and innovativ(in3d) while wipeout 2097was a successor.

edit:maybe best overall ever:mario64,great gameplay,great variety,extremly innovativ,but i don't like mario that much and I Don't really like jump'n'runs.