I am indeed very familiar with all of these projects. While they might sound excessively related, most are as unrelated as two different Adobe products.
Everything being open, each site has its own community of developers and its own crazy amount of custom tools, most of them unadvertised and hard to find.
I support keeping all of the tags mentioned in the question.
- wikivoyage: Tools specifically for Wikivoyage
- wikimedia-commons: Tools specifically for Commons, one of the world's largest media repository. Most Commons editors use desktop and mobile tools for media upload/management
- wikidata: This one too is rich in custom tools. Wikidata is on the verge of becoming the pivot point for most data mashups projects, so I predict the number of tools and libraries related to it will continue to rise exponentially in the next few years
- wiki: Any software that uses any kind of wiki syntax
- mediawiki: Extensions for the software called MediaWiki
- wikimedia: This is an umbrella tag for all Wikimedia sites that do not have a tag yet, for instance Wiktionary, Wikipedia, etc. And also for the special tools/services that exist across these websites but not in the MediaWiki software