Transmit is one of the applications that does this. It's kind of infuriating.
The long and short: Some programs will, if you run them and try to access a remote volume when it is not mounted, create a file in the Volumes folder with the same name as the remote volume. So next time you mount the remote volume, it adds a number at the end.
Solution, short of finding the programmer and beating him with a stick: be very careful not to run apps and look for files on a remote volume when the remote volume is not mounted.
