1) Combine english syllables to come up with a fictitious word that sounds good. This is how Ninite was named and they even provide the source for the program they used: http://ninite.tumblr.com/post/620277259/how-ninite-was-named... There are some other tools to help you with this: http://wordoid.com/
2) Jam two words and/or numbers together. They can be somewhat or totally unrelated. Examples: 37Signals, RocketDog.
Neither of these techniques gets you a name that is related to your project (you can loosely relate to your project with the second technique), but I think that's the least important part. Mostly, you just need a good domain and to sidestep any trademarks. Using a single cool sounding word seems like about the worst angle you can try from a legal/financial perspective; no matter how obscure you think it is (e.g. town names, latin words), it's probably been used dozens of times by others.
One of my startup ideas was a company that did this for you. It's not especially hard to do anything of this but it is tedious. It's not a very good idea in retrospect.