My love for Yojimbo knows no bounds… except that it got abandoned by Bare Bones. They’ll argue that it’s not abandoned, but it’s not like it’s kept up with the times either. I tried for years to get them to make an iPhone app for it, I even offered to make one myself, but it went nowhere. Sadly, Yojimbo is destined for the scrapheap of once-awesome apps.
EagleFiler is my “everything bucket”. I can put every kind of file in it and EF will find it faster than Spotlight. My main EF library is an archive of non-current files that I want to keep. Recently I found a drive with thousands of files that I had saved years ago. I dumped the files into EF and it only imported files that didn’t already exist in my library. It’s a “Swiss army” app that does a lot of things.
Although I’m hot sure how folders are represented behind the scenes in a DEVONthink database, you can also simply drag DEVONthink folders out of the app and into the Finder, and it will maintain the structure.