Neon Genesis Evangelion - For all of the reasons mentioned in this thread. It's spectacular in more or less every way.
JoJo's Bizarre Adventure - The art is gorgeous, the story isn't half bad, and it does all of that while being utterly ridiculous. The anime hasn't truly touched on the 'Bizarre' part yet, but it's pretty much a 1:1 adaption of the manga, so I'm gonna go ahead and recommend you watch the anime and then continue Parts 4+ of the manga.
Clannad/Clannad After Story - I'm gonna be honest here: the first season of the anime is kind of a mess, in large part due to the fact that it attempts to tell multiple VN routes at the same time and ends up being weird and harem-ish. With that in mind, I'd recommend the VN over the anime. That being said, After Story's adaption was fantastic and I actually preferred it to the AS route of the VN. It tore my heart to pieces. In short - the first arc's adaption kinda sucks, but After Story more than makes up for it. Whew, that came out longer than I expected.
Puella Magi Madoka Magica - gorgeous anime with (excellent characters, a great soundtrack and an awesome story. Personally, though, I hated the 'epilogue' movie (Rebellion) since I felt it tarnished the original ending, but I'm apparently in the minority with that. It's not like my opinion is gospel or anything. Still, I'll go ahead and say Rebellion is optional, and if you thought the original ending was perfect (as I did) you can give it a miss if you like.