In the course of a few day sampling, using btcguild and its ability to find 1/3 of blocks may seem better than something like slush which is hours between blocks, but over the course of weeks or months, the variance will fade away and it will become obvious which pool is keeping several percent more of your potential income
Slush is 2%, BTC Guild is 3%. BTC Guild pays for orphans. Comparing those two you'll end up with basically the same payout, except WAY smoother on BTC Guild.
EDIT: And BTC Guild pays NMC which Slush doesn't anymore. That alone is a more than 1% increase in income, completely making up for the 1% fee difference without even factoring in the orphan blocks being paid out as part of the 3% fee.