For many years I have used an addon in LibreOffice called “bookmarks” (Lesezeichen in German), but it became unfunctional. I could help myself a bit by using the KDE filemanager within LO, which offers a list of often used folders (bookmarks). But that still means browsing through folders to get to the right file. A while ago I reverted back to OpenOffice, where the bookmarks addon still works. But OO has its own flaws, and besides some files I would like to access outside of the office software with the proper app (like pdf’s with okular).
I figured that using an independent app which allows storing links to files and presenting them in an orderly manner (which I can configure) would be nice. I looked for bookmarking softwares and found only those who make bookmarks for webpages, or store its lists in clouds, which I don’t want. For webpages I have the bookmarks in my browser, for those I don’t need a separate app. What I am looking for, should be solely for files which are spread over my hard disk.
Just to give you an impression: I have more than 100.000 files on my PC, and maybe 100 to 200 of them are listed in the OO bookmarks addon. I could extend this list easily to 1000. As I am growing older, it is hard to remember filenames, thus just searching for the filename wouldn’t help.
I thought kbookmarks could help, but that is integrated into konqueror and also only for webpages.
If any of you have an idea what could be a good app for what I am looking for, I am all ears. If not, I’ll consider programming one, but before I’ll start on that, I want to make sure that nothing of that sort has been done until now. 
For your further info:
I am using Manjaro testing with KDE, all up to date.
You could simply create a folder named Bookmarks and symlink files you want there. You can organize them further by creating sub-folders and so on.
However, this feels like a useless task, because the work to organize bookmarks/symlinks is just the same as organizing the files in proper folders. You could logically find the one you need and if there will be some trouble, you can use “search” option in Dolphin, providing you have an idea how the file is named.
You decide what files go where, so basically bookmarking of files feels like an additional layer that gives no added benefit. Except some files that must be in certain places (like Steam files), that may need symlinks for easier access, the rest depends on you.
If you have thousands of files, this is a heavy task, which you have to adjust with time.
I personally prefer to work with one folder and then organize files once in a while. It’s not perfect, because sometimes I forget the logic behind the previous choice and can create a similar folder elsewhere, so similar files land in two places. Or I forget where I put it and then have to look through the folders, searching for logic where it would go. In most cases I can find a proper file, so that’s a success, but sometimes I do need to use the Search option.
Ah, one more thing. Dolphin has option to add tags to files, so this could be some alternative system of organizing files in one big folder. I personally don’t use it and prefer to have folders instead tags, which I find more convinient.
Obsidian is firstly, an app designed to manage markdown files; and it’s very good at that, with the ability to link internally to other markdown (and text) files in a folder hierarchy. I greatly recommend it for those familiar with markdown, and who want a very portable way to manage information.
Obsidian doesn’t handle PDFs by default, however, a range of plugins are also available, for example Better PDF Plugin, and other useful tools, which make it a worthwhile consideration. If pandoc is also installed, that opens up even more possibilities for document generation.
Additionally, this app is available cross-platform, which is a distinct advantage when working with disparate computing environments.
If you see potential in Obsidian, note that Zettlr has similar features and capabilities. Most others I’m aware of tend to be glorified note-taking apps, or editors, rather than document management tools.
I hope this information proves useful. Prost.
I use Dolphin’s tags feature, as suggested by @michaldybczak, to bookmark files. I think Baloo needs to be running to do this - I’m not sure if file tags are stored by Baloo or Dolphin, but I assume Baloo. The tagged files are easy to access afterwards - I just added to Dolphin’s toolbar the “Add Bookmark” & “Bookmarks” icons & then bookmarked the tags.
All tags can be accessed in Dolphin by navigating to “tags:” in the location bar (so make sure you bookmark the tags: page). Individual tags can be accessed via “tags:/tag name/”.
Here’s a screenshot showing both a tag in Dolphin & the configure toolbars popup to add bookmark icons:
Thanks all for your input. I greatly appreciate it! I will check out Obsidian and the Dolphin tags feature. Just a few comments to the suggestion by @michaldybczak:
The idea of creating symlinks is intriguing, but I wonder if I can name the symlinks different from the original filenames? I know that it’s up to me to use a stringent naming procedure, but I discover e.g. that I have files with more or less the same name in different folders for different purposes but very similar content. Just one example how this happens:
I have a folder in which I store all tax related files, and I have one folder in which I store all business related files, and in both are files which relate to my car and thus have the name “car” (it’s only an example). Today, I would probably do it like “taxes car” and “business car”, even though this would be redundant, because the folders are already named “taxes” and “business”. But I realised along the way (I use the computer since the nineties) that this can become helpful. To rename all files which I need to access now and then may be an option.
I use also kfind which I find often very useful, but then it happens that I have a bunch of files in the list, some of which are irrelevant, maybe even backup copies, and only one among them is the one I’m looking for. Thus, searching by using the tools available on the system isn’t really helpful (yes, sometimes it is).
I believe I have developed a good filing system over the time, but it still suffers from former mistakes I made, when I hadn’t realised yet how many files I would store (I’m sure some of them I can get rid of, but to decide which means going through all of them…).
Yes. 
man ln
That manpage has been criticised for excessive brevity recently
(not posting a link because: 'tis a silly place )
Source documentation may be more informative - ln invocation (GNU Coreutils 9.4)
We knows, Preciouss. We knows.
Let’s not go there.
As others already posted, yes, they can.
Note, that instead symlinking files, you can also symlink folders. This is handy, when you have folders that fit in two places, or if you need to access the folder often from another place, but logically the original needs to be in another one. Such symlinks are typically needed for some time, then you can delete them, once they become useless. The original content will stay in the same place.
Yeah, that is the pain. That is why the good habit is to look up the files periodically and clean/organize them, so it wouldn’t grow to unmanageable proportions. Still, I am at fault to neglect this, so when I do this job, I get too many of them, so it takes me some time and there is always more to do… So once in a while (once a year or so), I get some general review and cleaning of what I notice (not everything, but what is obvious, but sometimes look inside files to determine the content and then often I find them not needed anymore and in need of deletion 
).
In the past, I also segregated files by the type. Now I know it’s useless on the long run, because I can have many types for similar purpose and the purpose is what matters.
I try to create some general categories then smaller ones and so on. Basically it’s a logic system, which works, but usually only if I use it from time to time. If some things are left too long, I forgot the logic and need to re-organize things to the state that satisfies me now.
In your situation, using tags seems to be a solution, although the flaw in it is, you will lose it in other DE.
In your situation, using tags seems to be a solution, although the flaw in it is, you will lose it in other DE.
Not necessarily. Something I read a while ago about tagging was in the back of my mind, so I just looked it up. The tags are stored not by Baloo, but on the file system using extended file attributes (xattrs), so any indexer/file browser which can read extended file attributes should be able to display the tags.
Many operating systems (not just GNU/Linux) can read xattrs, although some might make you jump through a few hoops to do so.
Useful resources on tagging:
Using the File Tagging Feature in KDE’s Dolphin File Manager : kde
How to get the list of Tags dolphin uses? : kde (although I can’t find getfattr/setfattr in Pamac - not sure if there is an alternative available under another name)