Eastmean and Laird's original drawings have a special flair to them but since we're talking animation I'll focus on those.
Rated in order of awesome
1) TMNT 2003 Seasons 1-5
2) TMNT 1987 Pilot (there's something about those designs that I really liked, but it's only when they looked as good as they did in the theme song)
3) TMNT CBS Blue Sky Seasons
4) TMNT CBS Red Sky Seasons (edgier yes, and consistant more often but not neccessarily better than the Blue Sky CBS Seasons)
5) TMNT 2007 Movie (honestly I don't like the designs that much but they were well done)
6) TMNT OVA (the turtles and splinter looked good, April got a major makeover, Shredder... well... that was different but pretty nice none the less)
7) TMNT 80s Syndication (inconsistant and often just plan bad)
8) Back to the Sewers (could rise on the list potentially)
9) Fast Forward (yeah... a few things looks alright but I'd rather watch the bad animation of the syndicated TMNT seasons and that's saying something)
10) CGI Series Pilot (oh good heavens this looked awful)
Now we never saw how the designs looked as animation but the WB TMNT show designs weren't too bad. I liked the throw back to Eastman and Laird's old style. I'd say they're better than 80s Syndication design perhaps better than OVA design.