My ideas in a few words - in my opinion peppers are quite mild in flavour, so you could really replace by a lot of things, or even leave it aside depending on the recipe. But then again I love peppers :)
For reds : In both cooked and raw dishes, I would agree with tomatoes, though would not use canned. More like small crunchy tomatoes.
For greens : Probably courgette/zuchini
For yellow : Mild onions, or maybe a finely cut part of butternut squash