Trello works very nicely, also for project management within teams.
There are also free mindmapping tools, I have used FreeMind. It’s a nice way to store trains of thought.
Over the years, I’ve come to work with a sort of moving body of knowledge - as your thinking expands old ideas, knowledge and ways of working become less relevant and you only keep the things most valuable. To keep things as simple as possible, I just have a ‘notes.txt’ file on my desktop where I keep this knowledge that I need for my projects, and at the bottom I keep the most valuable knowledge and ideas from past projects.
Once I have too many ideas for the future I start discarding the ones less relevant to me. And the web+cloud is my repository.