Unity Mod Manager NexusGithub - Unity mod loader and manager
Harmony - Runtime C# patching library. Note: Comes bundled with UMM.
Assembly Publicizer - A commandline based tool to remove private and internal access modifiers
Publicise - A msbuild task based tool to remove private and internal access modifiers
Asset Extractors
AssetStudio - Tool for exploring, extracting and exporting assets and assetbundles.
UtinyRipper - Tool for extracting assets from serialized files (CAB-*, *.assets, *.sharedAssets, etc.) and assets bundles (*.unity3d, *.assetbundle, etc.) and conveting them into native Engine format.
UtinyRipperExporter - A commandline interface for UtinyRipper that provides dummy shaders and stable scriptstub and shader guid exports.
AssetTools.NET - A .net library for reading and modifying unity assets and bundles based off of the AssetsTools library from UABE.