I guess I'll answer my own thread and give the 
latest way I've set things up.

The front half of my cel book is devoted to 
artbook cels and originals.  The second half is 
Utena 'repros' (I take lots of liberties with my 
repros).  At the very end is where I store 
unfinished cels.  Dry ones, naturally.

I try not to have the same character on 'facing' 
pages.  I also try to 'match' the characters to 
each other.  Like I have my movie utena repro 
right below my Touga + kitty repro.  They're both 
chest-up eyes-shut and look good together.  And 
the matching utena/anthy cels from the op or ed I 
just finished last week are on opposite pages 
because they make a good 'set' too.  

So I guess my problem is I structure them 
aestetically instead of logically, which causes 
problems because it can be so much more 
subjective--one cel can change everything.  If 
you want to see some *REALLY* neurotic ordering, 
you should look at my book shelf, my paint rack, 
or my anime CDs. ^_^