Heck, just seeing Mickey and Donald on the same screen as Bugs and Daffy is a Real Life CMOA in its own right.
Even if it didn't work out, Roger barging into the Acme warehouse with a gun to try and save Eddie and Jessica from Doom's clutches is pretty impressive.
Doom gets one of his own:
Doom: The rabbit says one way or another he and his wife gonna be happy. Is that true? Eddie: Pal, what do I look like? A stenographer? Lt. Santino: Shut your yap, Eddie. The man's a judge. Doom: That's alright, Lieutenant. From the smell of him, I'd say it was the booze talking. (Eddie glares at him)
Eddie manages to get back at him good though with the good ol handbuzzer.
Even if this is meta, Bob Hoskins deserves some major props for his phenominal acting. He's TALKING TO AIR for about 95% of the time, but you honestly believe that the cartoons are there with him.
Judge Doom deserves a mention too. He is probably the only villian who can pull off a high pitched squeaky voice and make it sound legitimately threatening.
If you know anything about the legal nightmare of Disney and WB allowing their characters to be used in the film, it's a clear miracle that the movie was made at all. In particular, the two companies' properties had to share exactly the same amount of screentime, which is so smoothly integrated that you'd never notice unless you're looking for it.
Another star of the movie is simply the Visual Effects of Awesome. Never before has animation been so convincingly and brilliantly fused with live-action footage (with no computers, mind you) making cartoons actually look like they physically occupy space in reality. It really set the bar for Live-Action/Animation hybrid films even today.