First you need to know how each pool is paying - if it's PPS, PPLNS, etc... Most pools these days are PPLNS, meaning that they're paying based on what the pool earns, which is when a block is solved. PPS is paying just off of raw shares, so you get paid off the work you've submitted... PPS is pretty difficult for most pools to do, because if they are particularly unlucky and don't get a solve for a longer period of time, they have to pony up the money. Here's a decent writeup that shows all the different crazy payout methods pools use:
https://en.bitcoin.it/wiki/Comparison_of_mining_poolsWith PPLNS, it's much harder to compare pools - and you certainly can't do it in a 24 hours period, there's just too much variance. Really you have to do it for a week or longer to get any real idea... For example, let's say you have Pool A and Pool B, and on day 1 pool A does 150% over projection (because of luck), and Pool B does 50% (once more, because of luck) - you would say based on 24 hours that Pool A is better, because it paid you more, but the reality is they both are paying the same rate. The next day the luck might reverse, and suddenly Pool B is paying you 150% - it's just that when you're mining, everything is probabilistic, so over the long haul you should run at 100% of projection, but as you look at shorter and shorter time periods, like hours or days, it's going to have much more fluctuation.
This is also why people like larger pools - the bigger the pool, the more blocks that are being solved and the less susceptible to variance they are. Really I should be clearer about this - it still has the same variance, but because it's solving so many more blocks per day, it won't get 'stuck'. Back in the BTC days, sometimes smaller pools would end up not doing a solve for DAYS, and it was brutal for the miners, because they weren't getting paid - they start leaving, hash rate drops, and it makes it even HARDER to find the next block.