“Number 3 pencils and quadrille pads.”
Seymoure Cray (1925-1996), when asked what CAD tools he used to design the Cray I supercomputer; he also recommended using the back side of the pages so that the lines were not so dominant.
In 2004 Danny O’Brien did hold a presentation called “Life Hacks: Tech Secrets of Overprolific Alpha Geeks”. In this talk he showed his conclusions of looking at very productive computer programmers to find out why they are so productive. One important conclusion that I can only concur with is that the best people create or modify their own tools.
Be it self-written shell scripts for programmers or a personally adapted idea infrastructure in general (my words), but modifications are often necessary to produce on a very high level, both quantitatively and qualitatively.
I think this is also the reason why some programs fail the creatives who want to work with them. For example, a few people have tried to use a Wiki to collect their ideas and many have given up. I can understand this, given that the only reason why a Wiki works for me is that I have adapted it to my needs. Some adaptations are just the way the Wiki is structured, others (like the Ferret Frame) are more basic (see also here and here). But without these adaptations, using a Wiki would be pain in the ass (e.g., creating pages by making a link first, manually writing the standard contents of a page, writing tags manually). But with these adaptations, the Wiki is fast and usable — for me. I create pages by entering a name and checking a radio button in which directory the page should be created, I use templates which transfer on the blank page by the click of a button, and I click on tags in my tag list to assign them to the given page.
Whether this works for you or any other way to collect your ideas, you will likely have to modify your tools. Otherwise, finding a collection method that really suits you is a hard to impossible challenge.