Painter 12 - my favourite drawing program, nothing beats it in texture, drawings also look natural as opposed to digitally looking etc, I don't use it for cel-shade stuff though.
Photoshop CS3 - for cel-shade and all other quirky things, like formating, typefaces, placing shapes and logos into illustrations
Inkscape - used to make logos and designs intended to be scaled and placed into illustrations (opensource program like illustrator)
Manga Studio 4 EX - toning mainly, oddly I prefer Painter 12 to ink with over MS, I'm trying to convert though
Sai - for random doodles and warmups, it's stupid fast!
I also use Xpadder and DS3 Tool so I can use Sony's Playstation Nav controller as a tool selector, like D-Pad UP = zoom in, D-Pad DOWN = zoom out, analogue stick controls brush size, home button is ctrl+s, L2 Trigger is eyedropper tool and L1 is move tool, etc.
Played around with manga studio, its fun but i have yet to draw ANYTHING that looks half way what i want it to. Am i able to open files in MS so i can ink them and add then to the panles?
You can go to File > Import to open files into MS for inking, at least that's what I do (I use Image).