Sites that submit to "100's" or "1000's" of search engines are to be avoided, IMO. They are submitting you to FFA's which could actually hurt your ranking by being an irrelevant site linking to yours. I read that somewhere that is an authority, and with link-relevance ranking going on, it does make sense.
The most you'll get out of FFA's is plenty of spam.
http://www.ineedhits.com is pretty decent. It saves your profile for you, then kind of holds your hand while you choose one by one, the search engines you are going to submit to, out of a couple dozen search engines. The submissions are done one by one, and any search engines that require something a bit differen is detailed for you. I was pretty impressed.
It includes most of the major ones, and once you're done there, you can go manually submit to the two or three that are left.
Another one that seemed ok is
http://selfpromotion.com/I use these, and they've saved me a bit of time. I'm sure there are plenty more that are okay.
I occasionally bump things up by dumping a few bucks into overture, but if you choose to do that, familiarize yourself with their system before you dump hard-earned cash on something that can eat it very quickly if you don't know what you're doing.