Wow, quite a few series that I might have to check out............eventually. Aside from the ones mentioned below, I haven't really explored the genre and there are only so many 'harems' outside of it. Might write better descriptions later. Also, not in any particular order.
1) Rosario+Vampire (manga)
A harem series by default, with a much better manga story than the anime adaptation. Starting out as a more comedic highschool manga, it turned slightly more series over time. Heartfelt at time while exploring the relations between humans and yokai in their world.
2) Sekirei
Another harem series by default, a battle manga that has some real touching moments. As some people have described it "Pokemon with boobs"--although every Pokemon is an event mon. 'Last one standing' style competition with superpowered alien girls.
3) Martian Successor Nadesico
I'm not sure if it would count as a harem series, but Akito's (Main character's) 'harem' does count for much of the romantic aspects of the series, although not ever really the main focus. A real robot series where all the MC wants to do is be a chef, but he keeps having to get in the cockpit to fight the 'alien' threat.
Funny bonus is that when the series was adapted into Super Robot Wars BX, that a girl from another series even seemed to fall for the main character (with Akito even playing a role in recruiting/unlocking her later)
4) Shitsuriken
A little known short manga series that isn't technically a harem, but does feature strong hints of multiple females being interested in our heroine. Twisted school where a game controls several aspects of student life----also a tiny bit like Pokemon.
5) 123Change
Another little known series that might technically count as a harem, if a girl with multiple personalities counts as a harem (though one or two other girls might become interested, so it counts either way). Mostly a fighting manga that manages to include a good degree of realism. 3 personalities with 3 different fighting styles.
@CrossImpact TLR Darkness actually ended? I thought the author would find some way to continue it.
@Another Retired Shipper You might have (temporarily) retired from shipping, but even you must have a favorite harem or two.