I used to do my work with Photoshop CC, but I'm trying to look for ways to cut Adobe's Creative Cloud out. Manga Studio 5 is a great replacement for photoshop in terms of illustration. I've done some color with in it and I started doing pages of my comic as well. There are a lot of great tools for doing illustration: perspective grids, various rulers, a brush engine (similar to photoshop), text and comic bubble tools, and the ability to use a 3D mannequin (with prebuilt poses) and 3D objects. The fill tool and reference layer are nice for doing flat coloring -- the fill tool is WAY better than PS CC -- you can fill to the edges and with reference layers you can put the fills on another layer without much hassle. Inking is very smooth and I got used to the interface after using it for a few months.
I also use Blender for pre-vis on some comic panels. I made my own low-polygon mannequin and rigged it in Blender -- I learned all that junk off of Youtube videos. It's janky but it gets the job done.
I use my iPhone camera or my nicer camera for reference photographs or I hunt through google images or books at my library.
For script writing I use Scrivener on the Mac. For notetaking, web clipping, etc., I use Evernote and the notepad app on my phone, that way I can always jot down ideas and todo items. For my graphic novel's homepage I use Wordpress with a custom theme I wrote from scratch and I use Dreamweaver as the IDE and test locally with MAMP/XAMPP.