I don't post WIPs anywhere. I have yet to write a designer diary (although I'm sure that's in my future as my games get announced). The way I share my progress in my designs with the community is through updated prototypes and playtesting. But just because I'm not posting about my progress doesn't mean I'm not tracking it.
I essentially keep design journals. I have a handful of notebooks and each game gets a section of a notebook. I scribble ideas, work out thematic elements and component distribution. I list elements to implement in the future. I also keep a list of possible publishers. I transpose anything I write on loose pieces of paper to keep my thoughts in one place. My journals are combination workbooks and records of design progress.
As I playtest, I will rewrite my playtesting notes into my journals reordered to emphasize actionable suggestions/complaints. Then I write out a list changes I plan on implementing and check off that list as I complete items. I will go back through my notes to see if initially discarded ideas will work once the game is in a different shape. I am often surprised how much feedback ends up making its way into the game months after the feedback was given.
I reference these notes when writing rules, making component breakdowns, building prototypes, etc. Eventually, I do shift to writing my notes in a word doc. My digital notes serve two purposes: shareability and editability. Those files tend to be rulebooks, changelogs, full component descriptions, and flavor text scripts. Other than rules writing, which I do fairly early and often, all of these files are generated through discourse with an interested publisher. Otherwise, if I need to write something down it goes in one of my game journals.
I'm pro-writing-by-hand, but that's not the point of today's post. My first point is that keeping notes in one place is practical and useful. You can even use those notes to write a designer diary post if you so choose. My second point is that keeping useful notes doesn't have to be complicated or high tech. I'm a firm believer in graduating to more sophisticated programs only when you need them. I'm not going to spend time learning project manager software that I don't really need at this juncture.
Lastly, I want to throw in a good word for note apps on phones. They aren't the best use of memory for long term storage, but for short term they're a game changer. I have become a much better playtester by taking notes on my phone while playing a game. It enables me to give more detailed feedback and more accurate impressions of how I was feeling at certain points in a game. I picked up this habit from my local design group and I'm hooked. But I take notes for the game I'm testing with paper and pen.