IMO Wine develops a lot faster then Cedega. Cedega just had a head start and focus on getting only a handful of features/games working. It's not that I dislike Transgaming that much (although they did get lots of stuff for free), they're just a bunch of people making a living and they do give back some patches to Wine occasionally.
When it comes to getting games working in Linux I prefer the open-source model of Wine though. Being able to help out and try some community patches can be really fun not to mention a lot faster then waiting on Transgaming employees. They'd have to get it scheduled and approved, then someone has to run out and buy the game before they can start on it. I've heard they had some TG Beta program running now though, but to me that feels a lot like donating my work/time while they make money from it.