Your question is actually the subject of what is a pretty hot ongoing debate. Kind of like the whole digital versus analog thing. Much of it is subjective, but there are camps out there who believe that a real mixer has better "summing" (another way of saying the finished product will sound better if mixed on a console).
Other schools of thought will tell you there is no difference. Others even say your software will deliver a better mix, since you're not running your signals throught all that extra circuitry, thus introducing even more noise. Also, you're not putting everything through yet another digital-to-analog conversion, only to be converted back to digital yet again for the master.
If it's any consolation to you, there have been many commercial releases and hits you hear every day on the radio that have been mixed completely within the digital domain (usually with pro tools), using software not a whole lot different (in theory) than what you're using.
Personally, I can't comment, since I have absolutely 0 experience comparing anything done on a multi-gazillion dollar console with what I currently do with Cool Edit Pro.

Still, one can make a very good argument that there are at least some advantages to working with and manipulating a mix strictly within the digital domain; mostly in terms of flexibility . . . and of course I don't think I could live without the "undo" funtion
