I am a big fan of both games, but to be honest, I would choose Ratchet and Clank. Don't get me wrong, J$D is great, but the only game I liked was the third one. For R&C, the whole series is awesome. The commentary is hilarious, and the action is non-stop!
I'd have to say Ratchet and Clank, since both are more involved in the game than Jak and Daxter. And they have a more fun multiplayer too, so Ratchet and Clank all the way!
Ratchet and Clank is the best, but dont ever buy Size Matters for PS2, its just really stiff, the controls and jumping and all, you jump up, and then shoot right down basically, and he walks weird. The controls weren't redone to well to go from PS2 to PSP. I have Jak 3, but I cant beat the thing where you ride that weird little spaceh=ship thing in the tube, so I don't like it that much.