I personally use Photoshop for the panel layout and text, and Sai for virtually everything else.
You picked the perfect time to ask this question. I use Manga Studio (clip studio) 5 and the company that makes it is offering it for a ridiculous price of 15 bucks at the moment. Jump on this, it's pro-level software for comic-making. Here's a link to the deal.
I always use 2H mechanical pencil to sketch out everything. After scanning I use Paint tool Sai for all the lining and detail. Eventually I add the text and extra effects with adobe photoshop CS5
i use paint tool sai. it has a very old-school design, but the tools themselves are brilliant! you have loads of possibilities for brush settings, and you can create really artistic effects. ive been approached by people wanting to use what i use many times, which is a good sign.
for an example of one style with which this program can work you can check out my art here5
Manga Studio 4 Expert and Photoshop CS5 are what I use. I used to use just Photoshop but the inking just seemed stale. So I draw in pencil, ink in Manga Studio, color + shade in Photoshop. A lot of the fine tuning is done by my girlfriend in Photoshop as well.
Honestly it depends on what you want out of a program. Manga studio is an amazing drawing program and it is easy to make lines look fluid and interesting. Photoshop is a work horse for all your fine tuning and fancy bells and whistles. For me it is making static bars and adjusting colors and aspects I want to change.
What I need to learn is tones in Manga Studio. Does anyone have a tutorial out for that?
I use Manga Studio EX 4 for my comics, and Photoshop CS5 for resizing the pages. If I want to do anything in colour, I use Photoshop and Clip Studio Paint instead.
I'm also curious about tones in Manga Studio. The selection there seems quite lacking (unless I've been looking for them in the wrong places).
There are a bunch of tutorial videos on Youtube, and posted on Smith Micro's website, I believe, which do a decent job of explaining the basics of how the program works. There's at least one video covering tones, so that might be a good place to start.
I use Photoshop when I make comics. When I'm away from my computer, I make comic drafts on Autodesk Sketchbook on my phone. I also dabbled in Sai and FireAlpaca, but I'm more used to Photoshop's interface. But! I found something really interesting.
I stumbled upon a free program called MediBang Paint11. It's software made by the same developers as FireAlpaca, and the features are similar. However, there are 2 main differences that I find intriguing.
1. Cloud Storage. You can collaborate with other people by sharing a project together.
2. Multiple Platforms. It comes in Windows, Mac, and Android. You can have MediBang on your computer and a mobile device. Add the cloud storage thing, and you can do your comics anytime, anywhere.
I only got this program a few hours ago, so I don't know much about it and I'm still experimenting. But omg, I'm geeking out like the ultimate geek over this. xD
I primarily use Photoshop cs5.5. I also like to use Zbrush and blender3 (a free, open source 3D modeling package) to make 3D mock-ups and "digital maquettes3" (test sculptures for lighting and figure studies). If you're knowledgeable in 3D enough, having your own personal hand-made 3D reference for characters with complex shapes in perspective really cuts down on drawing mistakes and boosts production time.
Clip studio paint. There's also design doll, which is the best posing software I've found. http://terawell.net/terawell/?lang=en11
I will draw traditionally, then scan it into my computer, then clean up, arrange and letter with Gimp. It's actually been the easiest program to use. I have krita, but essentially, they are both the same, but krita has better brushes if you want to go pure digital.
Am in love with Manga Studio 5! Also, it is on sale this weekend for 15$
Once I got used to it, I find the interface EXTREMELY customizable and the comic features are wonderfully handy. Inking and painting is very smooth, and the oil/Blend tools are remenacnt of Sai.
For panel layouts, script writing, and lettering/balloons/captions, there is nothing better than Comic Life 3. Period.
Now, CL3 does no art. You will wind up doing that in another programme, but for everything else you need for putting together a comic, or publishing it, Comic Life is the best programme I have tried. It has drag and drop lettering directly from your script, over 100 pre-set page layouts, and you can customise to your heart's content, or build the page from scratch. It takes all of your fonts, and makes them immediatly available for you, and lets you drag, drop, and autocrop your panels. It's easy to use, and I have not seen any better way of layout or lettering.
Eagle
(And no, they are not paying me!)
I'm using Ubuntu, so there's no plenty of softwares to use, not even 'professionals', I think.
I'm using only free software: Krita, GIMP, AzDrawing, AzPainter.
I've used SAI up until this point, it's really great for all kinds of drawing except for lack of text (had to paste that over from GIMP) Plus there's no good/easy way of drawing frames so had to do that in another program too.
Recently got Manga Studio (thank you, 15$ sale!) and planning on using that for my comic from now on, it's pretty nice
9 days later
I mostly use Clip Studio Paint ^^ (Clip Studio Paint is the same as Manga Studio 5)
if your still searching for a Program I made a list a while ago with all the Programs I know and the prizes and so on 
All my work, comics and stand alone titles are created utilizing Macromedia Flash 4. Highly outdated, however it's perfect and streamlined to the point I don't even use anything but the mouse and keyboard to create just about anything. If you can find a copy, it will be pretty cheap but I'd say it's worth it to make things like this.
I used to use adobe flash but just made the switch to paint tool SAI
(its a good program and all, but I liked flash way more, but this was cheaper and its gotten pretty positive feedback from everyone I've seen with it. And its way cheaper (like 50 bucks) than flash (I was really just using trials when I had it))