"Best way" only applies to how you want to present
them (if at all), obviously.. I store my cels WITH
their pencils and/or backgrounds, but separated 
with either a) tissue paper (between douga and 
cel), b) a cut up cel bag (for backgrounds or 
layers), or c) double-bagged (cel in a bag, taped 
to background in a bag). The bagged cels then go 
into a cel book. Some people store the douga 
separately (like another book, or even just in 
files), and some together, that doesn't really 
matter...

This "cel-bag-book" setup is best for occasional 
viewing, large storage capacity, higher protection
from ambient light and environmental variables, 
and easier transport. 

You'll want to frame only if a) you REALLY want 
to look or show off the cel a lot, b) have a 
relatively protected area from too much direct 
light, and c) are willing to put in the time, 
effort, money, and learn how to take care of 
framed cels (framed cels take a little more care 
than merely slipping them into a celbook, as 
they theoretically require airing). 

Then there are the thin sliding drawer filechests
normally used for archived paper products and 
textiles in museum environments, but I really 
don't think anyone has this setup. (Does anyone?) 

Hmm.. Dunno about the paint-sticking thing, but 
I guess Sonia answered that one fine. ^_^

However, I would like to make a distinction - 
when a pencil or any paper is stuck to a cel, it 
is *not* necessarily stuck forever. There *are* 
methods of getting it off >;D, but not to be
tried without a fair amount of research and first
tried on a lesser cel, or take it to a cel 
restorer - and being fully prepared to lose the 
paper if necessary... 


More: [shameless plug ^_-']
http://www.oion.net/plug/qnd/cel-supplies.htm