When deciding which mining pool to join, you need to weigh up how each pool shares out its payments and what fees (if any) it deducts.
There are many schemes by which pools can divide payments. Shares are a tricky concept to grasp. Keep two things in mind: firstly, mining is a process of solving cryptographic puzzles; secondly, mining has a difficulty level. When a miner 'solves a block' there is a corresponding difficulty level for the solution. Think of it as a measure of quality. If the difficulty rating of the miner's solution is above the difficulty level of the entire currency, it is added to that currency's block chain and coins are rewarded.
Additionally, a mining pool sets a difficulty level between 1 and the currency's difficulty. If a miner returns a block which scores a difficulty level between the pool's difficulty level and the currency's difficulty level, the block is recorded as a 'share'. There is no use whatsoever for these share blocks, but they are recorded as proof of work to show that miners are trying to solve blocks. They also indicate how much processing power they are contributing to the pool - the better the hardware, the more shares are generated.
The most basic version of dividing payments this way is the 'pay per share' (PPS) model. Variations on this puts limits on the rate paid per share; for example, equalised shared maximum pay per share (ESMPPS), or shared maximum pay per share (SMPPS). Pools may or may not prioritise payments for how recently miners have submitted shares: for example, recent shared maximum pay per share (RSMPPS). More examples can be found on the bitcoin wiki.
The other factor to consider is how much the pool will deduct from your mining payments. Typical values range from 1% to 10%. However, some pools do not deduct anything.
Starting to mine with a pool
Having decided which currency to mine and which pool you'll work for, it's time to get started. You need to create an account on the pool's website, which is just like signing up for any other web service. Once you have an account, you'll need to create a 'worker'.
You can create multiple workers for each piece of mining hardware you'll use. The default settings on most pools are for workers to be assigned a number as their name, and 'x' as their password, but you can change these to whatever you like.