It depends on what kind of scanner you're using as well. Some, like the Epson 4990 that Ryan mentioned (same as I have) actually scan from both sides (which is why the lid is so heavy and has to be countersprung). Most of the desktop scanners that handle up to medium format negatives only scan from one side though, with a backlight in the lid, so I would agree that you would want emulsion side down, shiny side up in those cases. It's been a while since I've scanned negatives, so I can't recall which side I lay up. Probably whichever one makes a scan that I don't have to flip in photoshop to view correctly.
Ryan, on your comment about not having the templates for the various sizes of negatives to align them properly, I personally find it much easier to just lay the larger 4"x5" and 5"x7" negatives on the glass and align them by eyeballing it, then doing any fine correction necessary in photoshop. I just leave about an inch between the edge of the negative and the outside edge of the scanner bed, and can usually get pretty close. Sometimes I
might use the template/carriage for 35mm film, but that's more because they tend to curl more. Even at that, I'm often too impatient, and will just straighten in photoshop (since I can do that quicker than I can fumble around with the scanning template).
I do know that it's a very good idea to wear gloves while working with the negatives though, as fingerprints on the emulsion surface are nigh-impossible to remove (I imagine a professional would have ways to do it, but from my amateur perspective, better to just be careful on the front end).
Also I might note that, while it seems like it would be common sense to protect the emulsion surface foremost since that is where the image resides, I have on at least 2 occasions purchased negatives that arrived with sticky notes stuck directly to the emulsion surface.
Don't do that. In each case it appeared to have been done recently enough that the image was not affected, but I cringed when I pulled them out of their envelope.
Just a few notes from personal experience. Not meant to be professional advice
