http://www.youtube.com/watch?v=4CNldTbYy5A...feature=relatedActual man-portable rail gun being fired.
Notice the huge cloud of sparks that come out of it. Those are little bits of metal from, either the rails or the projectile that were stripped off by friction and superheated by the relatively huge electrical current passing through them.
And here is a 16KJ desktop rail gun being fired.
http://www.youtube.com/watch?v=hG7A29k4Oos...feature=relatedNotice the same cloud of sparks.
And here is an 8kJ pistol.
http://www.youtube.com/watch?v=GdYxzn8B9z0...feature=relatedOnce again, cloud of sparks.
It isn't as noticeable as a muzzle flash, but someone who is looking for it will see it.
Of course, these weapons have two things in common. They're made by amateurs and probably not to exacting tolerances, so one can probably reduce the spark effect with some effort. The other thing they have in common if that you have to plug them into wall outlets, severely limiting their utility where 110 volt outlets are not available.