what anime series differ greatly from their manga counterparts?

Ai Yori Aoshi, Elfen Lied, Kure-nai, Nagasarete Airantou, Rosario+Vampire, Sekirei, Suzuka, To-LOVE-Ru, and xxxHOLIC. I think season 3 of the Rurouni Kenshin anime was different from the manga but I can't really remember.

Kuroshitsuji...about halfway though the story changes *completely* from the anime. Both the anime and the manga are really good though.

Pandora Hearts...the show follows the manga almost dead on until the last few chapters that were released and then the anime (in episode 23) took a turn for the worst and I think they're going to try to complete it on their own where the manga still has a deep twisted plot that's going to take a while to finish.

Detective Loki...? The manga was more directed to teen audience whereas the anime was more for all ages Oo' [and Loki in the manga was a mischievous little kid and in the anime he's more of the calm/cool/smart character XD] Maybe Tsubasa Chronicles too...? [same, the manga's 13+ when the anime's all ages... Excluding Shunraiki and Tokyo Revelations though]

You may or may not like these series depending on your view of whatever you watch first. I'm not usually a fan of anime that seperate entirely from their source material.

~Kuroshitsuji

~Nabari no Ou

~Rozen Maiden

~DearS

~Zombie-Loan

~Galaxy Angel (and all of it's sequels/spin-offs)

~Black Cat

Monochrome Factor...

The anime is shounen-ai ("boy love") but the manga is completely un-gay. o_O Go figure.

fruits basket kinda differs and there are many more mange's in that series than there are episodes of the tv show.