Another source of lost coins is due to miners taking less than the maximum block reward which in effect "de-mines" an amount of coins equal to the difference between the allowed reward and the taken reward.
I'm aware of two coinbases that have identical hash to two others. This represents a permanent destruction of 100 BTC.
This is why version 2 blocks embedding block height were created.
What I'm curious about, and it's hard to check without software, is if either of the earlier in time of each of the two was spent before the later one was created. In which case the coins wouldn't be lost. I suspect they were unspent and lost, but it'd be cool if someone confirmed.