If you are strong enough to hold Wolverine underwater... he'll drown.
If you are strong enough to throw Wolverine into space... he'll suffocate and freeze.
If you are able to tie him up with rope or chains, whatever... you could starve him to death.
Wolverine's bones are unbreakable, but someone like the Hulk could pull his arm out of his shoulder socket. Cartilage, ligaments and tendons are flesh, not adamantium. Wolverine's head could be ripped off as well.