It's definitely a toss up for me. I think at this point I've seen The Melancholy of Haruhi Suzumiya more than any other series. It's pretty much my go to series whenever I'm down. It has it's issues, but I really like the characters
I've also watched both Boogiepop series and Bloom Into You many times as well
edit - adding D-Frag as well for feel good series I watch almost once a year
I've watched Utena all the way through twice, and I've watched big chunks of it way more than that. Plus the movie several times. I've watched the last 15 episodes probably 5 times.
FMA:B is something I've watched twice and I've read the manga several more times. Same with Death Note, which I do generally watch til the end.
Nozaki-kun gas been mentioned, but I've watched it probably 5 times, just because I've gone 'I want to see the Tomoda episode. Now I want to see Wakamatsu again.' I've only intentionally watched it the whole way through once or twice, but I've seen every episode way more than that.