Hammer 3.5 beta, essential over 3.4 if you use models especially
FJL's Expert FGD for Hammer
Merl's build of Zoner's compile tools, allows the use of the Null texture, and otherwise the best tools you can get for most uses
Half Life Software Developer's Kit (SDK), an incredibly useful heap of information
Milkshape modelling software
Half Life Model Viewer
PakExplorer for extracting files from PAKs
Wally for WAD creation
Goldwave for sound editing
ResGen for creating RES files

