Definitely take the rares out and sell those separately. People often are looking to buy rare's individually, so you'll get much better prices.
If you don't mind spending a bit more time on the issue, use your knowledge of the game to sort the commons and uncommons into which seem to be better than average and which are just typical. Look up the prices for those that seem good or are otherwise unusual online and perhaps sell those separately.
As to where I'd definitely check your local game store first as you'll get to deal directly with someone who has plenty of experience with card prices. If the owner won't buy them, ask if you can post a small notice somewhere in the store that you are selling them and give a brief description of what you have. Get a bit of word of mouth working for you too buy telling any friends you have that play that you're looking to get rid of them.
Finally, if none of these work, try to sell them on Ebay or an MTG dealing site. :D