Out of the preexisting ones, I use and want to keep X, Shift+C, R (palette and history are my two most used color choosers -- I also usually have a HSV wheel showing) Delete, Shift+Delete, Control+Delete, H, K, J, O, I, U, Ctrl+N, Y, E, Shift+Ctrl+S, Ctrl+S
I also use, but they're a bit cumbersomely placed on Dvorak: D and F. Or, huh, I guess they're fine. Weird, I've been using MyPaint for seven years but I never noticed that they're right above each other. That's great! I rarely use them together, though. I'll be zoomed in and think oh, I have to press D a bunch of times, or I'll be zoomed out and push F a bunch of times.
I also use Shift+Ctrl+P and Shift+Ctrl+O a lot, but I often hit the old shortcuts P and O by mistake. Which is weird, because I've also come to rely on O for rings.
My usage with these aren't to set a layer's final opacity (for that I use the slider in the GUI) but to distinguish two layers that are close to each other when I'm editing on one of them.
I also use Tab and I miss, I miss, I miss it in non-fullscreen mode so much!!! It was a godsend w/ dynamic tiling.
My most used shortcuts are probably Undo, New Painting Layer (above), and go to layers below and above, but I've got those mapped to non-keyboard input devices.
This list was very interesting because it showed me functionality I thought MyPaint didn't have (color blindness filters, paint modes) or had lost (Home, Show Layer Solo).
Let me add that I use , and . a lot and I wish GIMP, Alchemy and Inkscape would adopt them!