I am new to mining cryptocurriences but thought I would input my two cents and you can take it's worth just as that.
I mine at zeus and pooltobe's pool, I am only running a 460 gtx at around 100 gh/s and notice a small difference between the two. maybe this is because of the fee's I do not know.
But I could imagine what a small difference is at this low end of the scale, could become a very noticeable difference at a higher end of the scale.
I am currently on pooltobe's pool just to spread hash, it's not much but I figure spreading hash is the most important thing to help keep a coins health well.
The pool may display a difference in hashing power because the pool is making an estimate on how many hashes you are producing. Your actual hash rate is the one displayed in your mining software (cgminer, sgminer, guiminer, etc). So to answer your question, the only difference between the pools is the fee, and how fast it mines blocks.