With the current transaction fee rules, inputs of less than about 0.00005 BTC will cost more to spend than they are worth.
(somebody check my arithmetic, I'm good at dropping digits: MIN_TX_FEE is 0.0005 BTC per kilobyte, an extra input is a signature+pubkey+a few extra bytes = 100 bytes, so minimum fee per input is about 0.00005 BTC)
Wallet software should probably display micro-inputs as zero to the user (they really are worthless right now, since they cost more to spend than they are worth) and ignore them when computing the wallet balance or getting inputs to spend.