Old DSL cases would probably work for the console but any with game cartridge storage slots most likely won't accommodate the newer 3DS carts because of the nub.
Project Design generally has quality stuff, although their current selection of 3DS airform cases looks
rather tacky. I bought
a really nice PSP case from them which has worked wonderfully for several long-distance trips.
You could always go to Play-Asia for the usual Keys Factory or Hori stuff.
This is a link for the three Hori 3DS soft cases since Amazon.com only has black at the moment. If you want to use Amazon, you can find the
black and
blue hard airform cases there as well as the
black soft one.
I think hard cases are probably better for traveling and storage. You could use a sock or some simple sleeve to prevent scratching, but only the hard stuff has a chance at protecting from serious falls or being squashed or something. There's probably many other cases out there (silicon, snap, etc.); it just depends on what you want. The previously mentioned
Pull and Go Folio would have to suffice if storing a charger or larger amount of games is part of your criteria. It just depends on your own personal needs. A clamshell design is already enough for some people. =\
It is probably quite similar to
the blue one.
edit:
This is a link for the Executive Case for lazy people.