Here's my use case: suppose I have a potentially large number of users making transfers directed towards me (each using a separate account). My application will need to periodically poll the bitcoin daemon to find out what new transfers have been confirmed, so it can update the user's account/assets on the application side.
Two thoughts:
listaccounts [minconfirmations] (also new in 0.3.20, if I'm remembering correctly) will give you all accounts and their balances. If an account's balance doesn't change, you know it hasn't received coins.
And why do you need to periodically update the user's account/assets? Could you just query bitcoind for their current balance when they fetch their 'account status' page (or wherever you show the user how many bitcoins they have)? Are you doing something with the received bitcoins without an explicit action on the part of the user, and does that something care about the total balance or individual transactions?