Is there an open source tool to publicly destroy bitcoins? Several interesting applications of bitcoins involve a scenario where they are intentionally "destroyed".  Is there an open source tool that can be used to destroy bitcoins?

And if so, is it possible to programmatically verify (via the same tool or another) that the bitcoins have indeed been destroyed?
The most secure way to destroy bitcoins is to send them to a script that can never return true, and which includes the reference code that confirms the goal of destroying these coins. I don't know of readily available software tools that can do that, and I'm not sure the network will accept these transactions.

Here's a simple method everyone can try at home: Take the reference code, apply RIPEMD-160 and encode it as an address. Do a transaction which sends a satoshi to this address, and the the coins-to-destroy to 1BitcoinEaterAddressDontSendf59kuE.

To demonstrate my point, here is me destroying 1 mBTC - http://blockchain.info/tx/f374fb91ea29b02d295d535da537c7770caa71c4937095c51467b4d8b1b60c1b. Address is hash of https://bitcoin.stackexchange.com/a/7443/575.

Signing a message with the address used to send can also be employed as extra verification.