I just commited svn r197 (version 0.3.17.05); it is a "prevent possible security problems we haven't thought of" fix.
Before this change, you could compile your own version of bitcoin, create nonstandard transactions containing extra information or fancy new payment features, and all the official bitcoin clients on the network would happily include those transactions in the blocks they were generating and would relay them to their peers.
After this change, official bitcoin clients will not relay nonstandard transactions or include them in blocks that they create. They will, however, still accept non-standard transactions that do manage to get included in a generated block.
So, what should you do if you had a fantastic scheme for doing something fabulous with bitcoin that relied on the ability to generate nonstandard transactions?
1. Implement your fantastic new features.
2. Run it on the testnet to test it out. You can pretty easily generate blocks there, and, as said above, peers will accept your nonstandard transactions in blocks that you generate.
3. Convince the rest of us that your idea is great-- or, at least, convince a good percentage of the bitcoin-generating nodes that your idea is great.