Exactly two RPC calls can't be called when Bitcoin-Qt is running:
encryptwallet
stop
stop isn't yet implemented because there is work to be done to get the GUI and all of bitcoin's internal threads to shutdown in the right order (get the order wrong and we get crashes during shutdown).
encryptwallet isn't yet implemented because stop isn't yet implemented, and properly encrypting the wallet means re-writing wallet.dat and then shutting down cleanly so any database files are cleaned up properly (and any unencrypted private keys don't get left on the disk).
I'm not sure what you mean by "not available in any client" -- as far as I know, the original "Satoshi" client is the only one that supports the JSON-RPC interface at all.