I use the same handful of programs everyday to help make artwork on my computer. Here's a list of some of my must trusted applications and shortcuts.
Squarespace Note
Squarespace's Note mobile app allows me to quickly send text and images from my phone to my email. It does one thing and it does it really well. You just plug in your email address and everything that you fling from Note ends up in your email inbox. This is great for quickly taking a sketch from a sketchbook or scrap of paper and getting it onto your desktop.
Finder's Screen Capture (Copy Portion)
Command+Control+Shift+4 on my Mac lets me copy any portion of my desktop screen by dragging crosshairs over the area that I want to snag. This is really handy for quickly bringing low-resolution images like loose sketches or google'd photo reference into an application. When you select the area with this method, the captured portion of the screen is copied to your clipboard. You can then paste into an app, a chat window, or an email. I use it everyday.
Sketchbook Pro
While nothing beats pencil-on-paper for sketching, Autodesk Sketchbook Pro comes pretty close. I use it to elaborate on doodles that I've already started on paper. I often use the tools listed above to plop a sketchbook photo right into Sketchbook Pro. From there, I can use the respronsive brushes and pencils to tighten up the drawing with my Wacom tablet.
Illustrator
I use Adobe Illustrator for most of the heavy-lifting in my digital artwork. While loads of features have been added over the years, the original Pen Tool is still it's most powerful feature. Creating shapes and vectors has a learning curve, but nothing else offers the same level of accuracy and flexibility. I usually start with a sketch placed onto a layer and trace my linework over the sketch in layers. Then, I build up layers of flat color. Sometimes working in illustrator feels more like sculpture than drawing, but in a good way.
Manga Studio
Smith Micro's Manga Studio has made it into my regular process, following basic lines and color in Illustrator. With it, I can open open up a psd exported from Illustrator and continue drawing on top of it with the same vector-like smoothness, but with the control of my tablet stylus. In Manga Studio, I draw right on my screen using a Wacom Cintiq. It works really nice with a regular Wacom table too. In Manga Studio, I'm mostly touching up artwork and refining details, not making huge decisions. It's not part of the Adobe family, so the interface has some quirks if you're not use to it, but it's a powerful drawing tool.
Photoshop
While Adobe Photoshop remains an important part of my illustration process, I usually save it for last. After I've finished details in Manga Studio, I use Photoshop for subtle color-correction, lighting, and other small adjustments.
Others
Cocoa Potrace
Illustrator may have a decent "Image Trace" (aka Live Trace) feature, but Potrace is still my go-to for turning pixels into vectors. It only does black-and-white, but it does it really well.
Astute Graphics Add-Ons for Illustrator
Astute Graphics makes very powerful plug-ins for Illustrator. I'm still learning how to use some of them, but they are worth checking out, particularly the Widthscribe tool. If you've been looking for a flexible engraving look, this is it.
Frenden's Custom Brushes
Artist Ray Frenden is an expert at replicating traditional media with digital tools. His custom brushes are well thought out, and they just work how you want them to. I don't know how he does it, but his brushes are brilliant.