Aside from Boogie, there seems to be a distinct lack of 2k3 acknowledgement from this thread, which is the best animated series. It still wasn't as grimdark as the original Mirage interpretation but it had a nice balance of action, wit, and the occassional implication of fucked up shit. Baxter Stockman in particular spends the entire series incrementally mutilated as punishment until he is only a brain in a jar. Things did start getting weird in the later seasons, though.
The anniversary movie was a nerdgasm for me , the turtles teamed up with their 80s counterparts to stop the Shredder from destroying all the turtles timelines ( anime, mirage, live action, etc.) Lots of referential silliness and the occassional acknowledgment of the 4th wall.