Electronic – What are good quality of life additions to a prototype PCB

Forget category c: some things are truly disposable and can't be reused in their current state unless you want to start a recycling company.

Category B is the most interesting. For tools, there's eBay: just resell stuff you don't need. Even then, a lot of what we do is specialty stuff: I have 6805J programmers that no one wants even for the cost of shipping. They've simply outlasted their usefulness.

The problem with reusing hardware is the documentation has to be perfect, or the time spent trying to reuse a board or other hardware becomes more costly than simply starting from scratch again. I find that for the things I build for other people, I'm pretty good at keeping good documents. But for stuff I build intending to use for few days and then forget about, documentation is pretty much none existent, so boards end up permanently consigned to the junk bin.

Personally I usually power my prototypes from my bench power supply (it's an old ATX PSU). As you say, it saves picking a VReg at this stage.

Yes, you should have a nice meaty capacitor where the power enters the board.

On the times where I do want to have an unregulated power input to my prototypes (say a wall wart) I usually over-spec the regulator to use, so that I don't have to worry about the power requirements changing. I often don't worry too much about efficiency at this point though, and very often go for a linear regulator with heat sink where a switching one would be far better, but for a quick-n-dirty prototype it's not too much of an issue.

It is quite common for the power supply portion to be on a separate board any way - makes for a more modular system that is easier to design / redesign. Also if you are involving high voltages (well, mains - I know some of you don't think of that as "high") keeping it away from the main board is best as it means you can have the board running and not worry about handling it live.