Basket has been my favourite notetaking software for a long time, until I had switched to mindmaps. Quite recently I’ve discovered another use for it – a writing aid. Basket in one-column mode allows to rearrange your notes just by dragging them up or down (there’re keyboard shortcuts for that as well). When I’m writing a longer piece, I don’t need to hold a structure of the article in my head. I just collect all the pieces (quotes, blog posts fragments, my own notes, links, tweets etc.) and then rearrange it as much as it’s needed. When the flow of the thoughts is optimal, I start to connect these pieces by writing some text in between.
I don’t have DevonThink (I don’t have Mac) but for finding similar things in my archive I use SCAN. SCAN can aggregate content from a number of sources (it has plugins to read PDFs, OpenOffice and MSOffice files or even RSS feeds), analyze it, automatically assign tags, extract metadata etc. It has Lucene engine built in and does quite a good job of finding related pieces in the archive. It’s quite buggy, doesn’t read all PDFs (such as encrypted), metadata extraction doesn’t work as expected but overall the tool has a potential (and there’s no similar program available on Linux platform anyway). Its development was recently restarted so there’s hope it’s going to be improved in a near future. Additionally, it has a nice eye-candy – a visual overview of relations between tags.
This strategy is similar to the workflow described by Steven Johnson, but without DevonThink. So far I haven’t found anything better under Linux, but probably I need to check online apps – things do change every month.