If you want to permanently destroy the coins, there's really no way other than sending it to an address that's guaranteed not to have a private key, such as 1BitcoinEater.
Or you could read the thread and see there are multiple ways to destroy Bitcoins.
Coins can be mined out of existence (miner selects a reward less than the max allowed).
I wouldn't call that destroying them. Yes, it causes there to be that many fewer bitcoins in existence, effectively accomplishing the same thing as destroying them, but if the address created by the miner has less than the current block reward, the coins never existed, and therefore weren't destroyed.
Starting from 0.9.0 transactions with a single OP_RETURN have become isStandard (so will be relayed). If you really need to destroy coins use those, as they are provably unspendable (unlike funny eater addresses) they do not burden the UTXO set forever.
How do you get more provably unspendable than an address that can't be generated?