Update:
The EFF donation account/address was at mybitcoin, so half of them are gone.
I received 1,879 from the mybitcoin claims process. They are now safe in an offline, encrypted wallet; here is the transaction:
http://blockexplorer.com/tx/4b32ed2f7c1422ced7f1f0be88b2afe355c59180be72e942df085d93f1c8737a
According to block explorer, 3515.06 BTC were donated to the donation address I had for them:
http://blockexplorer.com/address/1MCwBbhNGp5hRm5rC1Aims2YFRe2SXPYKt
49% of that would have been about 1,722 BTC, not 1,879. I'm guessing the difference is because of donations from other mybitcoin customers just crediting the eff account without generating a block-chain transaction.
Before sending coins to the Faucet, I think I'll create a patch to always send "change" to the same address, so it is really easy to keep track of these bitcoins and make sure they're not sent anywhere other than the Faucet.