OP_RETURN can be used to store references to external resources, say for example very long meta transactions that don't fit into 40 byte, an asset contract or whatever. The storage pointed to could be a website which lists something like (for the sake of an example), a side chain or a P2P structure like a DHT. To my knowledge this was discussed several times, but never tested on a broader scale.
You know, an interesting question to ask yourself is if it's totally ok to just embed a hash of the actual data in the blockchain, and rely on the data itself being made available by some DHT or something, why can't Bitcoin itself do that to make blocks smaller and improve scalability?
Remember that Bitcoin would work just fine if miners didn't validate transactions if clients implemented client-side validation, as is done in Mastercoin and Counterparty, and to a lesser extent, Colored Coins. What's so special about actually putting those tx's in the block?