Neat question. Here are some examples that come to mind.
(1) I use Hazel rules, the DT web clipper, and file saving hygiene to grab any paper, blog post, website I feel is at all relevant to my research and archive it in DT. I also sync my notes from various services and apps (including my Tinderbox zettelkasten). This gives me a rich foundation to crawl when I have a need or curiosity. I can search all these documents for a phrase or citation and when I find something of interest, I can “magic hat/see also” it and find things I had no idea were related. For example, a book I’d read mentioned a historical movement I was researching, but become the book wasn’t about that movement, I’d never have thought to look at it for a reference. I know you mentioned that see also isn’t working for you and maybe, given your needs, it won’t. But I can imagine a scenario where I’d feel that way, too, if I didn’t realize how to use it specifically for my needs. For example, I can take a reading note and “see also” to find relevant articles to read that I’d never known about. This is possible because I collect everything of interest to me. It wouldn’t work well if I didn’t do that part. Also, I can query every article I’ve found at all interesting for a method or topic I wasn’t even considering when I originally collected it.
(2) I can create a group of documents and search across that group for further analysis. For example, I collected a bunch of papers about technologies that focus on mindfulness. I tagged them so they’d end up in a smart group and then I searched that group for references to Jon Kabat-Zinn to see who referenced his definition of mindfulness, specifically.
(3) Another way I’ve used smart groups productively is to collect a bunch of papers, drag them into Tinderbox and map them in relationship to each other. DT and TBX work well together so when I drag an item into TBX, it appears as the first page of the PDF and the item link is preserved so it’s easy to access later.
(4) I put rosters with my students pictures and names so that when they email years from now asking for a recommendation or favor, I can remember who they were.
(5) When I have a personal or family-related health issue, I collect papers and websites and put them all in DT. I can query across them and see what commonalities “see also” reveals. Impossible to do in ad-strewn crappy med-space that is Google these days.
(6) I can read, highlight, and annotate a file across platforms and have that annotated version with me on my computer, iPad, and phone. Also, my highlights and annotations are automatically smart grouped and searchable on their own.