If I recall correctly, the audio editor that comes as part of the Nero package has the ability for you to 'gather' a noise-print from a 'silent' part of the track, and then apply it, as a very selective filter, to the whole file. I've not used the Nero one myself, however.
A couple of (expensive) products can do this, and can quite effectively and selectively remove clicks etc., from vinyl sources too. They are Sonic Foundry's Sound Forge (with the Noise Reduction plug in). I prefer v 4 over v 5 for this. And Steinberg 'Clean'.