The brown wire is basically the source of all switched power on the bike. It goes into the junction box and feeds all the circuits that aren't always hot (I'm assuming a bit based on the PreGen/500, as the wiring diagram doesn't show where a few of the fuses are sourced from). The switched brown wire in the dash is fed off the brown/black wire from the Ignition fuse, which in turn should be fed by the main switched brown wire going into the j-box.
You could use the brown wire going into the junction box to trigger a relay, and feed that into the j-box in place of the original brown wire (to remove losses for any switched circuits) as well as running it to your accessories. The 500/PreGen j-box also has an unused Acc fuse and an output from the Headlight fuse that bypasses the turn-on-delay relay - I'm not sure how the NewGen compares.
The Main fuse is only 30A and the individual circuits are only 10A, so any standard automotive relay (usually 40A) should be more than enough for anything on the bike. Depending on exactly where you're going to mount it, it's probably a good idea to get something waterproof.
http://www.cycleterminal.com/accessory-relays.html