with chained up boy, torture whipped maybe locked up somewhere etc.

For starters:

Hoshi no Yakata - It's several volumes about an S&M club and its workers.

Sadistic Boy - Same author as Hoshi no Yakata. It's about a sadist school boy. Unfortuantly the scan group hasn't finished it (currently at v2 ch6) and probably never will since they announced they were disbanding a long time ago.

Love Prism - A brother with a serious sadist streak takes his brother as his slave.

Prisoner (KAEN) - A guy is taken hostage and treated like a pet. I don't remember it being as hardcore as the others, but still worth a read.

There's also another one I'd recommend, but I can't remember the name. If anyone else can remember, the uke is held prisoner in his own apartment by a guy who raped him in front of a friend. The guy later turns himself into the police as a serial rapist at the end of the manga.

Cogito Ergo Sum (I think, therefore I am)

^I agree with the aboved poster. Check those out.

Kibishiku Aishite
Bi no Isu ;D
Katayoku no Sokubaku - Maybe. I forgot what went on in that manga.

Try these mangakas out: Mizukami Shin, Chitose Piyoko(maybe), Chi-Ran and Kaen

One-shot:
Aka no ori
Eien ni Owaranai - maybe.

These threads may help. :3
1,2,3

Quote from leoak

There's also another one I'd recommend, but I can't remember the name. If anyone else can remember, the uke is held prisoner in his own apartment by a guy who raped him in front of a friend. The guy later turns himself into the police as a serial rapist at the end of the manga.

I think what you're thinking of is Sokonashi Freefall Romance, the Fantomless cage.