There's an id3v2 field, ETCO, that allows you to specify the intro and outro silence transition times.

I'd rather have something that worked correctly on-the-fly, instead of needing to fill out a tag. I'm sure that a cleverly-written piece of playback software could do it.

In fact...

I see a real market for a piece of software like that, in the lines that Rio currently has and is planning on for the future. I mean, if a Joe Sixpack sticks a Pink Floyd CD into a Jupiter or a Visteon unit, they'd be unhappy to hear the gaps.