I'll either reduce volume in between songs (in software), or use a compressor (also in software) after the fact, if necessary. I guess reducing volume is probably best as you'll preserve the dynamic range in the applause whereas compressing can make it sound kind of odd. Though, to be honest, I don't care as much about the sound of the applause, unless, as pfife says. I have an acoustic show I matrixed, and the applause during the songs - after a solo, or some such, is great and totally adds to the feel of the recording.