Currently, I use Copic multi-liners for all of my comic inking because they're copic marker resistant and water proof. However, each individual pen is about £5, nibs can be £2 each for the finer varieties, and the ink has a tendancy to fade when I rub out construction lines (whether this is the fault of the pens or the paper I'm using, I'm not sure.

I also dislike how rapidly the nibs wear down, making them a pain to keep replacing.

Do any DDer's out there know of other marker-proof liners that are available? I've seen people using micron pens that look effective, but I don't know if the nib is a felt-tip or a more plasticy nib like my copics.

I just switched to digital inking but until recently, these were the cheapest pigment ink fineliners I could find:
http://www.cultpens.com/acatalog/Uni_Pin_Drawing_Pen.html.
The ink from these things is never going to be as black or fade resistant as india ink, but that can be easily remedied once the pages are scanned. None of these pens will last you more than a few pages, depending on your style, but I found the nib wear useful because it allows you to get some line variability.

I also used a Pentel Pocket Brush (the best brush pen you can get), these markers for broader marks and medium fill-ins (similar kind of ink and they can be refilled):
http://www.cultpens.com/acatalog/edding_33_Paper_Marker.html
and for larger areas you could just have at it with a Qtip - cotton bud and ink, watercolour brush, or just do it with photoshop if you're a pirate, or the Gimp, if you're a cheapskate like me!

As Ironscarf finely suggested, I also highly recommend the Pentel Pocket Brush Pen. I got one a few months back in February, and I loved it.

I wasn't very good, but I loved it anyway.
The cartridges aren't that cheap, but not that expensive.

The only problem is the learning curve. It's not easy going from fine liners to brush. But once you get over it, and get used to using it, it'll definitely be worth it.

Which reminds me, I need to get back to practicing with it!

Oh yes, and for the black areas, you could either use a Q-tip and ink, or photoshop it in like Ironscarf also said.

OR, you can do it the medium-cheap way (because assuming you already have photoshop, we'll say that it's the cheap way), you could buy sharpies. There are a few problems though, like the ink isn't fully black (which can be adjusted in photoshop), sometimes the tip tends to flick ink across the page, but you just have to be careful. I can get about 2 sharpies for...1.75 at the dollar store? It's a great deal to me.

Also sharpies have a tendency to discolor the surrounding area over time. The infamous yellow! I've done my fair share of sharpie fill ins, though. Some of it has held up. Not sure if its the paper or what.

I concur about the pentel pocket brush. I got one a couple months back, and its my favorite thing ever! Like a brush, it takes some practice to make it do what you want it to do, but boy is it worth it!

It's the pocket brush pen thread all over again

That was a great thread wasn't it? Should've had a sticky.%)

Can't we just start a forum soley dedicated to how great the Pocket Brush is?

Or how about this "Hand Inked Vs. Digital Inked Vs. Pentel Pocketbrush"

hmm... waaaaaay off topic.

We really should.

I actually gave mine another chance today.

Wow. I think this gave me the greatest results ever.
So yes.
Buy it.
Buy it over every other possible option.