well here's what I've found so far in my trials, one.. scan in color, b/w scan's will almost always jag up your lines. 2.scan huge, at 300 or so dpi, then when you shrink it to 72dpi for posting it will generally get fairly tight.
When you're cleaning your image use the levels control sparingly, it is awesome to take out light bits of trash but it can start to get really jaggy if you go to far with it.
What I've finally decided on for my comic is to start inking digitally, I use flash or illustrator .. haven't decided which I like best (probably illustrator though) Also flash has a really nice option to turn a jpg into vector, when you do it it will smooth all your lines when it turns them into objects... I can't recall the function off the top of my head but I used it in
#14 on the devilandted. It is pretty functional just takes some playing around with.
++Edit++
ok the function in Flash is called trace bitmap, basically you import your image into flash (file > import > import to stage) then run modify>bitmap>trace bitmap .. fiddle with the controls to figure out a setting you like, I suggest working with a fairly large piece when doing this I found I got better results that way.
If you have a tablet though, I would really suggest trying out inking digitally. You scan in your pencils then go to town on them in a vector based proggie (or photoshop.. it will give you nice smooth lines as well.. just not quite as smooth or easy to much about with as one of the vector tools).
--Steve