Funny, I never really thought about this before. Alright, I'll give it my best shot...but ranking something like this is kinda tough for me...
1. Mirage - Original series. Ninja turtles as they are intended to be. What more can I say? The original run was great. I loved the grim art style, sense of family and adventure, and most of all the basic charm it just had.
2. Movie Universe - These were what I was watching most as a kid...the OT of course too, but these little vhs tapes were what always kept me coming back when I was younger, and still to this day, as dvd's

. To be honest, I'm mainly speaking of movie's one and two. I think the first one did a great job of adapting the mirage universe in a style acceptible to hollywood. This movie is just classic tmnt. I also have a soft spot for Secret of the Ooze. Someone on the forum actually mentioned something a while back about how the first movie was a great Mirage adaption, and SOTO was really just a great OT adaption, and that really struck a chord with me, once again upping my appreciation for SOTO. We kinda got both universes on screen within a few years of eachother. Pretty cool. The last two movies, I can enjoy, but aren't too memorable for me.
3....Tie.....It's super hard ranking all these, and I dont think I could past those top 2 lists. The original toon was my bread and butter as a child, and I definitely hold a soft spot for it....Especially the First season, which was totaly quality cartoon making if you ask me. 2k3 series...Really great compared to
most cartoons coming out these days, and a totally great add to the tmnt mythos. I look forward to watching seasons 1-4 as they are released on dvd, and catching the episodes I missed, and basically just rediscovering what is so great about that show...It's been a while since I've seen some of those season 3 and 4 episodes.

....As for everything else...it's all great. Love Image, Love archie, love etc...they are all fun in their own way. I never mind seeing the tmnt interpreted in as many ways as possible. They are so flexible.