Well, Im a digital gal, so this is how I do it.  
I do the lines using a computer program, usually 
Illustrator since that's my favorite program. You 
can also use Pshop too though, it just takes a 
steadier hand :).  Then, if you want to avoid a 
lot of the mess you get with pens, pens and paint 
mixing, wobbly lines, you take the line art to 
Kinko's, or a blueprinting place and have them 
printed on the cel.  Ive done this, and it always 
turns out great.  Granted, it's not the artsy way 
to do it, and you dont get quite as black of a 
line sometimes, but even in Japan they use a 
special Xerox machine to line their cels. Some 
places do them better than others, I strongly 
suggest a blueprint office.  Also, it's best to 
paint on the backside of the cel, and leave the 
lines on the front side.  Take your original line 
art, make indications of all the shaded areas, 
details etc, and make a reversed print of it.  
Use this as an underlay to paint your cel's 
backside, that way your lines remain on the 
front, and you have no problems.  Sounds 
confusing doesnt it??  I havent painted a cel 
since college though, I find it way too damaging 
to my nerves as I dont have the patience for it 
anymore ^_^;;.  Good luck to you though!