While ikiwiki supports hierarchically categorising pages by creating SubPages, that's often not flexible enough, and it can also be useful to tag pages in various non-hierarchical ways.
Since this is a wiki, tagging is just a form of linking. The general rule is that all tags are links, but not all links are tags. So a tag is a special link that ikiwiki knows is intended to be used as a tag.
Generally you will tag a page without putting a visible link on it. The tag plugin allows you to do so, like this:
[[!tag mytag othertag thirdtag]]
You can also tag a page with a visible link:
This tag will be displayed just like a regular WikiLink.
One way to use these tags is to create a blog of pages that have a particular set of tags. Or just look at the BackLinks to a tag page to see all the pages that are tagged with it. Plugins can be written to do anything else with tags that you might desire.
Once you have tags, you can use the pagestats plugin to generate tag clouds.