Both BTCGuild and Eligius are good options. I first started out on Slush's pool last year, when I was noob miner.
Oh Slush's pool with that crappy stratum proxy batch file you had to run for block erupters....memories.
How about GHash ? Is not it doing good lately ?
Usually try to stay away from the larger pools. Though unlikely, you never want to contribute to the possibility of a 51% attack.
Is it the fact that large pools pay less to its miners ? Apart from 51% is there any other reason not to mine at a large pool ?
It's like doing your part in this thing.
One of the concepts of Bitcoin is it's decentralized. Decentralized currency, technology, protocol, servers, nodes, teams working on it, etc...
As long as you're contributing your hash rate to one of the larger pools, you're making Bitcoin more centralized. I just mine at the smaller pools as a matter of principal. Principals aside, whether you mine at the smaller or larger pools, it evens out in the end due to variance.