For PDFs, references and notes I highly recommend using an app that can assign tags―several for an item, of course. Preferably, tags themselves should be organizeable at least in a hierarchy.
You won't create a good collection of tags right away, but you'll grow and groom it over time. It's important to assign tags to new items as soon as they come in. Gradually, you'll learn what words you actually use when you're looking for something, and those will become your tags.
I can't recommend a specific app right now: I happily used one that begins with 'E' but alas it went to shit.
Also not sure about the merit of any software for tagging files. I know that some say good things about TheBrain as evolution of the mind maps idea, and that it apparently can link files in its data, so you could try that.
I know it's kinda pricey, and not everyone can afford it. But if you can, Evernote is actually pretty great for PDFs and tags, etc.
I didn't 'get' it for the longest time. But I moved from one country to another, and I didn't want to bring all my paperwork around with me. So I bought a scanner which can scan duplex (both sides), and a red stamp which says 'Scanned'. I digitized everything except super important things like (birth cert, etc). Tagged it, and it sits in Evernote. I've been in many situations where I am at a business or company, and someone asks for X document, and expect I have to leave to get it, but I can whip it up on my phone and mail it to them if needed.
I scan my bills, and the payment receipts, etc.
I keep copies of paystubs, etc.
When I start projects I make a new folder under my existing 'Projects' notebook, and I can put everything related to it in there.
With premium, it also scans through the PDFs and can help you find things when you need them. Again, I know not everyone can afford it. Just pointing out that, if you are in a position where you can, and you could use this kind of functionality, I find it super helpful.
Last tip, use the 'Scannable' app (iOS at least). You can scan documents (very well, surprisingly!!) on the go. For example, once I got roped into signing a new contract for a phone plan. I didn't want to carry all the paperwork around all day, so at lunch I used scannable to send it all directly to my Evernote, and shredded the originals.
Not affiliated either, just a fan who likes the software.
Yeah, the problem is, basic functionality like text editing and even just scrolling keeps getting worse, slower and more broken with each version, at least on Mac. Display of web-clipped pages and images becomes buggy. The desktop app somehow gets bugs in its window switching behavior. The Android app is slow and heavy like a glacier, can't save data on an SD card, fills all internal storage to the last byte if there are too many notes to sync (incapacitating the phone), and needs lots of memory to edit simple text notes.
Meanwhile the developers are fiddling with the interface to keep up with MacOS, and the company is adding more useless front line layers to the support to shield itself from the customers. And this all has been going on for years.
And for Android users, CamScanner is a great scanning app. It turns quick cellphone photos into great, clean, auto-cropped scans that it can then bundle into PDF batches (great for grouping receipts by month, for example). The free version does watermark these files (small text on the bottom right of each page), but it's a great app otherwise. I've even used it to scan family photos from distant relatives while traveling and it's worked great (no watermarks on photos, just on the PDFs it renders as far as I can tell).
Qiqqa is a great program for managing a PDF library. It does OCR, full text search, shared libraries, cloud libraries, bibtex for citations, tagging, and doesn't choke on massive libraries.
You won't create a good collection of tags right away, but you'll grow and groom it over time. It's important to assign tags to new items as soon as they come in. Gradually, you'll learn what words you actually use when you're looking for something, and those will become your tags.
I can't recommend a specific app right now: I happily used one that begins with 'E' but alas it went to shit.
Also not sure about the merit of any software for tagging files. I know that some say good things about TheBrain as evolution of the mind maps idea, and that it apparently can link files in its data, so you could try that.