I've written out something that can be used on the server side, it's in PHP.
https://github.com/Bit-Wasp/multisig and the demo is
http://multisig.thomaskerin.tk /
http://multisigtestnet.thomaskerin.tkI've added an electrum library to there, because you should deterministically generate your sites keys from a master public key, and keep the seed on another computer. But the code currently just creates a new keypair, imports it to bitcoind immediately in the mean time. This is only really because in the code, so they only need to sign once on top of the sites signature.
Sending to P2SH addresses is a problem - users will probably have to use bitcoind/qt or electrum. So is signing, but
https://coinb.in/multisig will do all that for you in a nice way.