I'm not TK last time I checked, but when it comes 
to piecing multiple scans of a cel together, I've 
done it with maybe half of my collection since my 
scanner is so small that not even a regular sized 
cel will fit entirely on it.  :P  I use Photoshop 
now because layers make it so easy, but when I 
was just getting started, I used Paint/MGI 
Photosuite.  Photoshop allows you to rotate if 
the scan is a bit crooked, though it's best to 
get it right the first time, but with programs 
that don't have free transform functions 
(selecting part of the picture and rotating only 
that part), the biggest keys are to make sure you 
scan the parts with the same settings and that 
you pick one end of the cel and keep it perfectly 
parallel to one edge of the scanner so that when 
you piece the two  scans together, they fit 
together.  If you've got that down, it's as 
simple as resizing one of the scans, and pasting 
the others in.  Also, overlapping scans is a good 
thing.  It's all a pain, but it can be done 
without $600 Photoshop ($300 educational edition! 
heh heh).  I haven't even attempted the two cels 
that are both longer and wider than my scanner, 
though.

~the red hood, dreaming of getting a newer, much 
larger scanner