I used a BAS marine grade system I got on E-bay on my ST1300. Used my Pioneer XM Inno1 with it, and it sounded great. If you're after a deck and mp3 etc, there's lots of choices. Mounting systems are getting somewhat scarse though. Back in the day there was Cyclesound and lots of others that made mounting consoles to fit just about any kind of fairing around. I've seen the odd Honda/Clarion type I-III selling on E-bay etc too. Thank goodness for google.
I'm also looking at replacing my Cassette/AM/FM system on my 1996 GL1500SE. I would like to swap it out with something I can plug an MP3 player into it. but if need be I'll bite the bullet and see about mounting a Stereo in one of the compartments with maybe a 6 pack CD changer. I really don't want to lose out on the space.