tl; dr: If you distribute your hashrate among multiple pools in proportion to their respective total hashrate, your variance will be as if you mine in one pool with the total hashrate of all pools.This is a point I was trying to make in
AoBPMRS (section "Proxy mining") but I get the feeling people miss that so I import it as a forum post.
Mining pools are used primarily to reduce variance, and the larger the pool, the more effective it is for this purpose. There is a simple way to decrease the variance further: Mine in multiple pools. For example, if EMC is 450 GH/s and Ozcoin is 700 GH/s you should use 40% of your compute power to mine for EMC and 60% to mine for Ozcoin, and then your variance will be as if you mined for a single 1150 GH/s pool. It doesn't need to be exact, of course; if in this case you do a 50%/50% split, it will be like a 1100 GH/s pool.
This not only helps variance for individual miners, but is healthier for the network. In the current standard usage, there is a "the rich get richer, the poor get poorer" tendency where larger pools are more attractive and thus grow even larger, and all else being equal, the equilibrium is a single huge pool (thankfully, all else is not equal). If miners adopt the proposed strategy, the tendency will be to maintain the status quo distribution, so pools can rise and fall based on their merits. Miners will enjoy the low variance of a single huge pool, without the centralization of power problem.
I'm not an expert on how to technically implement this but it shouldn't be much of a problem. If you have multiple GPUs you can simply point each to a different pool. I think there is local proxy software that allows you to split your hashrate between multiple pools, and if not one can be made.
Miners will probably not want to bother with creating accounts in many pools so will only use 2-3 pools. Ideally, there will be proxy pools that optimally distribute hashrate among as many hopping-proof pools as possible, allowing miners to enjoy low variance with a single pool account.
Appendix: More generally, if you put a portion of p1 of your hashrate at a pool with total hashrate H1, and so on, your variance will be like in a pool with hashrate of 1 / (p1^2/H1 + ... + pn^2/Hn). That the optimal value of H1+...+Hn is obtained when pi = Hi / (H1+...+Hn) is left as an exercise to the reader.
Pools which have other advantages (for example, take less fees or absorb variance with their reward method) should be given a higher weight than their hashrate indicates.