How do you document your hardware design decisions?
I personally go the old-fashioned route: I have a design notebook where I write down absolutely everything about the design decisions I make. Especially component and value choices, current calculations, power supply calculations, everything. I also document software/firmware decisions and notes on timing and resource usage. 

Each notebook has a contents page to reference a specific part of the design (power supply, etc) and all the pages are numbered.

I have considered going digital a number of times but it is nice to have my notebook out in front of me while I work and I find writing formulae digitally to be quite awkward. It's much easier to write calculations out by hand.

When preparing a spec or formal documentation for a board design, I usually refer back to my notebook as a refresher of what I did (or I write the digital documentation at the same time). Even though this may seem like I'm doing the same thing twice, I find that my notebooks are pretty much all calculation and explanation for myself, where documentation is much less verbose and much more formal and explanatory for others. As such, I don't often find I'm writing the same thing twice.