Transaction with slightly changed script is never relayed
The standard client will not relay non-standard transactions. However, if you get them directly to a miner that accepts them, clients will process them correctly and the transaction will work.

You can send your transactions to 173.242.112.53. This is a server run by Eligius that will relay all valid transactions and they will include even non-standard transactions in the blocks they mine. Others who are willing to relay or include free and non-standard transactions also tend to link to this node, so it can get your transaction included in blocks mined by other pools as well.