You can use a simple tool like this [1] (mine) to check the balances. You might have to split into two session with 100 addresses each in order to avoid the API to ban you. After you know which addresses still have a balance, import the private keys into a wallet you are not usually using, preferably something slim (Electrum, Multibit, etc.) or online (e.g. blockchain.info) and make a single (or more so you dont link those addresses) TX to an address you are currently using. Blockchain.info offers a sweep function after import. Id just make a new wallet there, import the keys with balance, selecte sweep after each import, transfer the coins and forget about that wallet.
[1]
https://bitcointalk.org/index.php?topic=736607.msg8355029#msg8355029
