Only bitcoind/qt. Electrum supports paying to them, but does not support signing. Best thing you can do is train your customers to use
https://coinb.in/multisig - which handles keypair generation and signing. It's a very nice tool. I've tested it out, it's useful as once you pay to the multisig address, you can do all the rest in your browser without messing with the bitcoin client any more, since all you need to do is sign, which is stateless and doesn't depend on the blockchain.
If you want to try implement a multisig system, I've written a basic one in PHP.
https://github.com/Bit-Wasp/multisig