IGN has thrown together a number of great "Top 100" lists and this is no exception. Most of the list is drawn from Marvel and DC, but there are a few independent press surprises. The top 10 is filled with the usual suspects, but the order is always up for debate. It makes me want to put together my own list, one not based on impact or popularity, but instead based on personal preference.
Head over and check out the Top 100 Comic Book Villains.