Anything counts as long as the tooling API was critical to the functionality of the project. This includes Andrew Fawcett's Apex wrapper around the API.
Just about any tool that is built for Salesforce developers will touch the Tooling API for some or all of its functionality. The Metadata API alone can't perform all the operations that the Tooling API can. More common would be to use a combination of these two APIs and then some (Streaming API, Partner/REST API, Bulk API)
Here is an extract from Tools for Development that I know for sure use the Tooling API:
- Force.com IDE – plugin for Eclipse
- MavensMate – plugin for Sublime Text and Atom and VS Code
- FuseIT SFDC Explorer - This is a standalone tool (Built by myself and distributed via my current employer)
- Welkin Suite – This is a standalone tool;
Even the Developer Console uses the Tooling API for a majority of its calls. It is also used with the Salesforce DX command line.