I’m a huge supporter of tags and would prefer to stick with them exclusively. With a small change to the "submit resource" user interface it might be possible to solve the issue of hundreds of tags that fit one "category" (such as "plugin", "plugins", "add-on"). An idea that just sparked in my head was to have a managed list of tags (created by the admin) and an input box below the list for additional tags made by the submitter. Upon saving the managed-list would just be merged with the user-generated list.
Keeping the tag philosophy means that a single resource could belong to any number of "categories". I shudder when I hear the word "category" because in my mind it means a resource can only belong to one "category". When users hear the word "tag" they immediately know that it can be found in various ways.
The display of the Resources would still remain extremely flexible, simply display the managed list of tags for the start page, adding an "Other" link to the bottom of the list that goes to a view showing the next most popular tags in a list (no clouds).
I created a mockup of what I have in my mind to be the start page for Resources. It might merit some explanation: I tried to avoid using the word "categories" for the reason stated above;
tags should only be one word (managed tags have a summary shown on the home page).
Update: Also, ignore all the design elements, I’m just working on content.
Here’s the mockup:
MODx Resource Repository Mockup