In my brief research, it appears that in most cases it's okay to name a piece of software the same name as another existing piece of software as long as it's in a different market.
Does that seem true?
For example, I see several with the name 'Coda', and 'Eclipse'. And those were just the first two names I picked to try.
I have name for my software that I think really fits well, and it is in use by a couple other small-ish pieces of software but they are in totally different markets. Of course I'm hoping my software will make some waves, but I'm not expecting to be the next Microsoft (nor would I want to be ;).
How much would you worry about this?