The newest thing in comics, is an unfathomable possibility. Keeping your own vision, and doing your own comics!

It used to be that you would either be an independent artist or a mainstream artist.

The independent comic artist would create their work, self publish, and try desperately to get it distributed. They didn't call them underground comics because they managed to rise up to fame and glory with a million fans world wide. It was difficult, especially in the time before the internet.
The Mainstream comic artist, would be sending in script samples, doing art tests and trying to make connections to break into the industry. They'd end up on a team working on someone elses comic. Or if their story was accepted, it may have been picked apart, parts re-written, characters removed, new characters added, until your comic story was barely recognized.

Now today, what with the glory of the internet you are able to read comics online, opening up the independent comic industry to the entire world!
Not only that, but some great printing services became available, so you would be able to create your own professional looking comic book that you could take to conventions or sell online and distribute to local stores.
Because of that, yet another great thing happened! There are now publishers that will accept submissions of fully created comics. You're whole comic, as you wrote and drew it, available through a publisher with no changes, all your own characters and your own art.
Using these labels to get noticed would open the door to larger companies finding your work and perhaps hiring you, or taking your comic under their label, widening your audience even further.

I'll get to a list of these available resources in a moment, first there are some things to consider before you get on the comic bandwagon.

There are A LOT of comics out there, online, in stores, both mainstream and Independent. Even now, this industry has a butt load of challenges. It's not easy to get noticed, and it takes a heck of a long time to get your name out there. If you want to be an independent comic artist, seriously, you need to understand it's a hell of a lot of work. You don't get a steady pay cheque like you would working for a company, your money is based on your own sales.

You have to be a 1 (or more if you have partners) person comic making machine! You have to network, produce, draw, and write (among other things) all on your own. A label will help get your name out there, but you need to build a fanbase beforehand. Theres a lot more to a comic than just drawing and posting. You wont be able to not do something you don't like or have trouble doing, because theres noone else but you and hiring people is expensive. When you get a comic printed there is a bit of production work to be done. Depending on what size and shape you want your comic in, you have to set up your files in a certain way before they can be printed. Your art has to be set up to fit those specifications.
While drawing on printer paper and posting them on DrunkDuck may get you a pile of fans right now, thats same tactic wont work for printed comics. What people will fan over for free and what people will pay for are two very different things.

First you should ask yourself if you have the time, the drive and the strength to do this. Will people buy this? Are you really contributing to the independent comic scene, or reinforcing that stereotype that it's all crap?
Just because you are doing it all on your own is no excuse to do this half-assed. It doesn't have to be perfect, I mean heck I've seen some pretty retarded mistakes on mainstream comics, we're human, but your comic has to look good. The story has to be good, you have to have it setup right and you have to dish out your own pocket money to do this, in some cases, a lot of money. Do you know about bleed? Trim? Live-area? Are you using the right size paper for the size of comic you want?
How much is this going to cost you? How are you going to advertise this? Where will you get your fan base?
Decide if this is the right path for you. Do you want it under another label or would you rather self publish and sell through something like Indyplanet alone.

If you're willing to go the distance, heres some basics you need to know:

Many of these creator owned publishers would prefer you to have an already established fanbase. It shows them that there is an audience for your work, and they'll just expand on it. The bigger fan-base you have, the better.
Some of them would like to see your work printed, as a comic, they don't want "pitches". So you'll need to get some copies of it looking nice and professional to hand out.

most of them will require you to have a couple issues already complete before they will publish your comic under their label. This is to ensure you wont just stop creating it, or loose interest.

You may still be required to do all your own work and pre-press work and you will have to share the earnings with your publisher.

If you don't keep it up your publisher could drop you at any given moment, and you'll have likely ruined your reputation. Reputation is everything, keep it clean.

Having said all that, you should research for yourself and get information first hand, see it with your own eyes.
You'll need to make sure you pick a publisher that works for you. Some will want a little editorial control, some wont want any at all. read the submission guidelines closely and ASK QUESTIONS.

Some publisher labels to look at are:

Arcana Studio
Dakuwaka Studios (black and white only)
Archaia Press
Ronin Studio

Look at the links pages of these sites. Links pages are a fountain of glorious information and connections. Research, find more companies and get yourself the best contracts.

Some printing companies to get some quality printing done are:
Ka-blam and comixpress

To build a fanbase, you can offer some pages or a chapter to read online and post it on one of the hundreds of comic network sites available.
This will give you a measurable fanbase that people can see. You can come up with an estimated number of readers and fans, increasing your chances of getting under a label.

A couple examples are:
Comics Space
thewebcomiclist
onlinecomics
Webcomics Nation
Hotwebcomics

To name a couple, check links pages on those sites for more and visit some of the comics on those sites and check out their links. That is how you find websites. Google is overrated, networking is where it's at.

This is just a small list and small bit of information and things to think about to get you started. You really need to (and I cant stress this enough) research for yourself, make your own connections and move under your own steam.