I wouldn't put Rugrats on my Top 50 at all. IMHO, Rugrats was a very overrated series. I personally never "got" that show, nor did I understand what was so great about it, I never found those babies all that funny. Plus I hated Angelica with a passion. All personal opinions aside, I think that Rugrats is too recent a show to be placed on the same list with Looney Tunes and The Flintstones.
TV Guide put the Powerpuff Girls on their Top 50, but a part of me is cynical enough to believe that the main (if not only) reason that they did was becasue the PPG movie was coming out that same month. If the Powerpuffs were going to be on the list, then Dexter from Dexter's Lab should have been on there as well. After all, Dexter's lab was the 1st Cartoon-Cartoon, not to mention the premiere World Premiere Toon. There would have been no Cartoon-Cartoons had Dexter's been a failure.