I normally don't do top 5 or top 10 lists, but just to change it up and make up for my sad lack of anime bloggage lately here goes. Thinking about this there are a LOT of potential candidates--slapstick in the form of the guy getting the stuffing knocked out of him by the bishoujo is pretty common.
#5: Keroro (Keroro Gunso) - Maybe aliens have a unique body structure that enables them to withstand beatdowns, but Keroro seems to be wrapped in bandages every other episode. Natsumi's usually the culprit but he also takes a beating from his subordinates on occasion, or the dreaded Nyororo. Although Keroro almost always deserves what he gets, so the pity meter doesn't register real high here.
#4: Chitose (Happy Lesson) - Being the plaything of five...unique...teachers makes Chitose's life a living hell. A funny living hell to watch, but probably not so funny when you're Chitose and Kisaragi-mama hits you on the head with a hammer. Chitose's got to have a titanium skull, otherwise he'd never have survived Happy Lesson, Advance, and Final.
#3: Urashima Keitaro (Love Hina) - Keitaro deserves a spot since he's at the receiving end of the Naru Punch in pretty much every episode of Love Hina, sometimes more than once. Usually he gets smashed through a wall and then knocked into low Earth orbit, and while you don't generally see him land it's safe to assume the landing hurts like hell too. Although like most abused anime guys, he never seems to actually get injured by all this, at least until Love Hina Again when he breaks his leg.
#2: Moroboshi Ataru (Urusei Yatsura) - Ataru takes a LOT of abuse, although my sympathy for him is diminished by the fact most of the time he clearly deserves it. In today's world, Ataru would probably be in prison for chronic sexual harassment, since he's always hitting on any girl he sees, and inevitably his pursuits end with Lum running 10,000 volts through his sorry skirt-chasing ass. But Ataru not only gets electrocuted by Lum on a routine basis, he also gets charred to a crisp by Ten, frozen in a block of ice by Oyuki, nearly chopped in half by Mendou, and gets slapped by every girl between age 9 and 90 in the Tokyo metro area.
And the most frequently beaten down male lead in anime is...
#1: Sakura (Dokuro-chan) - Sakura gets the #1 slot because Dokuro doesn't just beat him down when she's mad at him--she actually kills him, over and over again, and then resurrects him. I've never been killed that I can recall, but I'm guessing it hurts a LOT, especially when it's at the hands of Excaliborg, Dokuro's spiked club of doom. Although I have to wonder if Sakura's human because he seems to have at least a swimming pool's worth of blood in him.
And the Honorable Mentions...it was hard leaving them out of the list, but they didn't quite make the cut:
Kyon (Haruhi) - Haruhi doesn't actually punch him or anything, but mentally dealing with the SOS-dan is probably equivalent to one of Lum's electric lynchings.
Kawahira Keita (Inukami) - Youko fries him, destroys his prized ecchi possessions in front of him for maximum psychological impact, AND occasionally teleports him outside naked to be arrested and/or molested by dogs. Didn't quite make the top 5 this time, but if this keeps up for the rest of the series I might have to rethink things.
Saito (Zero no Tsukaima) - Seems to walk right into beatings, did he really think he'd get away with the "your breasts are zero" comment? I can't wait for the next episode, where during dessert he'll tell Louise "with every cream puff you eat I can see your ass getting bigger." I'm guessing he'll be whipped to death by the last episode.