I haven't really explored the harem genre much so I can't give many really. But one I do have is Rosario+Vampire. Key word here is manga though. I have only seen a couple episodes of the anime (and seen random parts of it otherwise) but as far as I'm aware the anime adaptation drops the manga's plot quickly and resorts to ecchi comedy antics, heck even the two episodes I saw had way more panty shots alone than probably the entire manga did.
But anywho, Rosario+Vampire manga (particularly season II) is awesome. It manages to fit in some good action, character development, and even a pretty viable plot in spite of looking like a random fanservice-centered harem. It's got the comedy and ecchi of many other harems out there (mostly in part 1) but it has the other elements of a good story too and in the long run I'd say that season II is really what makes it worth reading.
Some might also call Clannad a harem but it isn't really. There are many girls in the cast (more than one who have feelings for the protagonist; it is from a visual novel after all) but from the get-go it's pretty clear who the protagonist will choose and there's never any fanservice or the like as one might expect of a typical harem. It's an amazing romance/drama story though.
