I like to classify things by tagging them. But I find it much more useful if the tagging system has its own hierarchy. Unfortunately most note taking programs have flat tagging systems.
I am in the process of transferring some of my notes into InfoQube to give it a more thorough workout and see if I can break it 
My first attempt at making a hierarchical tagging system involved assigning the items in the hierarchy as parents to the topics (articles) and this works but it doesn't scale very well, it becomes cumbersome quite quickly so I wondered about using WikiTags (ugh ... what an ugly name).
If you make a hierarchy of categories and make each of them a link to a wikitag then assign that wikitag to each of the appropriate articles then you can click on any category in the list and get a list of all the topics assigned to that tag. The categories don't need any text in the HTML pane, thats what the articles are for, but they could contain explanatory notes if appropriate. This is when someone quotes this post saying this is nothing new and everyone else has been doing it this way for years !
Anyway this is how it looks on my laptop (I have edited the toolbars and other UI elements to cut down on things I don't need) :-
However there is a problem. On my machine at work, using IQ Portable on Windows 7 everything works as expected. On my laptop using the installed version and Windows 10 I have to insert a space after the text in the grid (after and not included in the link) or the formatting gets messed up.
Here is the dialog box to insert the wikitag link into the category without adding a space at the end of the text in the grid :-
And here is the problem, the entry has a bunch of extra text appear in before the entry :-
But the hierarchical tagging system works and is quite useful, the strange behaviour with Windows 10 is easy to work around.
Now if only there was a slick way of putting links to items into the HTML pane, copying the item ID number is definately not a slick way of doing things. 
Comments
I use a general tagging "system" using simple principles/rules that I can apply in many different situations (whatever the application, if text can be entered : Word processors, file names, etc.). The principles/rules are simple, but their practical applications has to be strict for them to work. Note that all the different combinations and uses can be fairly complex… That's why I use AHK to help me with the practical applications.
Although it feels like a pretty personal thing to share, I’ll explain parts of it (otherwise it’ll be too long)
1. The syntactic structure of my tags/categories
As it is now, my tagging scheme is built around the abcz abbreviation system.
1- "tgs" (a fixed string that indicates that the “word” is a tag — it could be something even shorter, like two numbers, but it has to be pretty unique… Otherwise, your searches might bring up a lot of undesirable results)
2- "X" (a capitalized letter which indicates a metacategory. I personally mainly use 2 letters here : "P" & "O", hence 2 metacategories.
3- "abcz" (the abbreviated theme, following the abcz system).
1.1. Short Explanations :
"O" characterizes almost any tag that is an answer to the question “what is it?”. These answers can be : it’s late, it’s a draft, it’s important. In other words, tags of this type have to do more or less with the object itself (the image, the file, etc.), its nature, state, provenance, the approach used, the format, etc.
"P" is for almost any tags, ranging from projects to themes, subjects, etc. It doesn’t answer the question “What is it”, but, rather, “what is it about ?”.
Following this model, here are some tag examples (just for illustration, won't go into too much detail...):
tgsOimpt (something important)
tgsOdrat (something that’s a draft)
tgsPthee (something related to theatre)
tgsPemon (something related to emotions. Note : in my abcz abbreviation system, I never use the plural )
etc.
Example: a text, an item or whatever, could be both important and adraft (what is it?) : tgsOimpt tgsOdrat. But also talk about theatre and emotions : tgsPthee tgsPemon. The four tags put together would be : tgsOimpt tgsOdrat tgsPthee tgsPemon
These tags can be placed in the category or wikitag field (or at the end of my strictly formatted file names in which all “info fields” are delimited by specific characters. But I won’t go into that now….) very rapidly… thanks to AutoHotkey (downloadable for free here)
2. AutHokey
So, to use all that efficiently, I use AutoHotkey autocomplete feature. Using AutoHotkey allows me to :
1- make sure I never ever make orthographic mistakes,
2- never use a tag that "doesn't exist" in my "registry",
3- easily search through my tags (just use "search" in my AutoHotkey script) which are classified hierarchically (easy to do in an AHK script),
4- easily add new tags or modify them,
5- have some tags to always appear together, grouped ; example : if I write "perl", I want AHK to write : "tgsOmi tgsOPERL" (which means : "something personal, written by me...)
6- only enter a few letter to have the complete tag
…etc. possibilities are… uncounted
Of course, I try to organize my AHK script so that it’s not too hard on the eyes and pleasant to use (with lots of commented lines -- essential)!