Beyond just the official mod tools and any art tools you might need, there are a variety of community-made tools that have become de-factor standards or enable new workflows.
For working with Blender, most people use either or both of the Halo Asset Blender Development Toolset (H1-H3) and Foundry (HR, H2A, H4). These allow you to export source data and some tag formats directly from Blender (depending on the target editing kit) rather than exporting to FBX and then converting FBX to source data formats using Tool.
There are also tools which work directly on map files. Reclaimer allows for the recovery of assets like models and textures from maps, while TagTool and Assembly can be used to edit tag values within map files. Generally you should be building maps from edited tags rather than "poking" tags within built maps, but it's worth mentioning these tools exist.
If you prefer to avoid command-line use of tool.exe, you may be interested in the Osoyoos launcher.
Cross-game tools
Game-specific tools
See also the community tools for Halo 1.