From my own personal experience I use a Sharpie. Better for the transfer from paper to PC to have a nice clean line. Just my two cents.
Mystic
Usually I just scan the picture straight in and out of my scanner/printer. Then, I ink the copy and put the original in my folder. I use digital inking pretty often also.
Similar to the gnome
1. pencil
2. Scan the picture
3. Play with it in Photoshop so the pecils are Blue
4. Print
5. Ink over the Blue printout (Pencils are stored intact in a folder)
6. Scan the inks
7. Play with it in Photoshot tp remove the blue
Not perfect but it works for me
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I mainly use ps, because have not learned how to do hand inking well. I have tried brush, fountain style ink nibs, and felt tippped pens.
Digital ink.
Back when I inked by hand I did it on vellum over the original so that I never killed a pencil piece.
Crowquill exclusively. No brush or anything. Ended up going through a LOT of nibs though, 'cause you really have to abuse a croquill to get the line variation you want, and you tend to snap one of the prongs off.
I pencil first, then I found a REALLY cheap-[censored] pen that you can buy 20 for $2 that makes a nice thick smooth line (Papermate 1.2 M ). That's what I mainly use for my inking (which is really just outlining). For chibis I use black marker, but I think I'm going to get some brush pens or something.
I don't ink at all and when I do, it's either been with a really fine point pen (the good kind not the Bic kind - not that you can't do great stuff with a bic, but I'm not that good) or Illustrator or both.
I use black india ink. Over copies of the pencils. Sometimes over the original pencils. But only if they suck.
Which is semi-frequent.
It's time consuming and difficult, but I never understand directional light like I do with a pen and ink in hand.... call me old-fashioned.
-SL
I have no black ink.
Who took it??
I have tried both analog and digital inking. I haven't used those ink-dipping pens yet (but will be as part of my class) and totally NOT looking forward to that.
But I have a bunch of various sized Micron pens, from the brush, 0.01, to 1 sizes. Lots of good line weight variation there. I really love the solid 'black' you get from them. Quite astounding. Just remember, I was just as scared as you were to 'mess up', that's why i usually worked on a photocopy of the original pencils. You can also fix any errors in photoshop later as well.
I have also digitally inked in photoshop with tablet. Lots more work, but comes out looking very similar. I actually did a Roxstar inking with both manual and digital, and side by side they're virtually identical.
Normal inking
Digital inking
No i can't make straight lines on the tablet 
Yes I know about using the 'shift' key.
So to each their own! 
Currently I ink in Photoshop. If it's a pencil drawing I am "inking", use the level tool until it's fairly dark and then just clean it up, through use of the polygonal lasso, the eraser and the brush tools.
That's fairly time consuming, however, so I think I will trying putting a layer over the pencil drawing and just trace it.
If I start with a digital sketch, I have a sketch layer and the line art layer over it. THis is a very new thing for me so it could change.
I used to used traditional pens. I used rapidograph pens and a variety of fairly cheep drafting pens.
If you do not like hoding a pen straight up and down because the position is too stiff, I wouldn't recommend the rapidograph pens for you then. That's why I stopped using them. Felt bad, too, because they weren't cheap.
I do both, depending on the situation. Tho' I haven't seriously inked a piece with the real stuff in a while, my method is usually to use a lightboard and ink on a fresh piece of Bristol with the sketch (or a print of the sketch) on a piece of paper underneath.
Otherwise I use Painter to ink, as for me it gives much crisper lines and control that Photoshop.
I have an assortment of ink pens, but I usually end up using an ink bottle and holder with nib for real ink stuffs.
@Liz!
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What brush do you guys use for digital inking?
I usually use the hard round, in very very small pixel sized, usually 3-7, and up to 14 on larger thicker lines, and I'm usually WAAAY zoomed in. Like... 300-400%
For general outline on digital I use 7 (meaning main body outline etc), for general details I will often use 5 and really fine stuff 3. For heavy thick line work around the eye etc I have gone as high as 17 or 19 or enev used the area fill function. Brush I use a round hard brush for inking.
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What brush do you guys use for digital inking?
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I use a non-airbrush with the opacity set to 75% or so. The size varies, depending on the line width but, on average, it's usually 10-12 pixels in size.
Like Rowr, I am usually zoomed in quite close, 200 to 400%.
I'm bad and have been just using a simple ball point pen. I used to have some really nice gel pens that I would use. But have been to lazy to go buy some more.
I pencil my drawings in, use a PITT ink pen, then erase the pencil lines. Works pretty well.
I don't understand how you can use technical pens for inking comic style work, let alone people who use a ballpoint or something like that.
How can you stand to not be able to vary line width by pressure? I can't imagine using anything other than a croquil dip pen.
I alternate between digital inking (I use Photoshop mostly, with a hard, small brush - 5 px for a majority. 7-10 for eyes. 1-3 for small details)
When I feel like dragging the lightbox out, I use microns to ink (I use a fresh sheet of paper over the pencil work). I generally use photocopy paper, since it has a nice, smooth surface to ink on, and is fairly inexpensive if I make mistakes. Which I'm known to do.
Overall, I prefer digital inking. Easier to clean up those mistakes
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I am loving the 5 adjustable "ink" tooks in Comicsworks... this is a study for my son's character - Lycari, a werewolf defender he plays with my namesake on Virtue.
Anyway, CW has 5 tabs that you can slide to your needs for weight, the ability to leave ink splotches, why you would want to I don't know, but it's soooo pressure sensitive, I'm thinking of putting it in my will.
LJ
Well if you use a pen with a fixed width tip, you have to basically go over your line over and over making it thicker where you want. Not too hard to do, and that's the way I work anyway
I was taught the oldschool methods:
1. Brush - I use a 00 or 0 sized sable watercolor brush to ink with, and then an acrylic ink (normally black)
2. Dip pen - croquill or Deleter tips
3. Faux sable brushpen - a refillable brush pen that's great for traveling.
4. For sketchy inking I use Pilot Precise V. I've used them for years and they are by far, the best pens for sketching, especially when paired with tracing paper.
5. For 'professional' work I normally ink in Illustrator (various versions) with the brush pen set to a custom setting for a closer effect to real brush inking.
Well if we're going old school, and you can still find them, try to get a lettering brush for inking. The tip has a sort of slanted edge to it like a chisel, and it makes amazing straight lines every time... as well as some even weighted curved ones with some practice. It's a brush used for calligraphy, so it won't be in the normal section... good luck mission art impossibles...
LJ
Do you use pen over the pencils? Ink on a sheet of paper overlaying the pencils? Digital inks?
I'm sketchy (get it, sketchy?) about using inks that aren't digital because of how permanent they are. What do you use?