i think it also depends on the amount of the transaction. for example, with a transaction under 5 btc, then 3 confirmations is good. if the transaction is over 1000 btc then 6 confirmations would be safe to verify the deposit. if the transaction is < 1 btc then i'd say 1 confirmation would be enough.
I think it would be best to wait for 3 confirmations even for transactions <1 btc. For transactions > 4 btc then 6 confirmations will be enough. That's just what I'd do.