Below is a list of software I use to create maps and various other files.

Hammer 3.5 Beta - This is a beta patch which you place over the Hammer 3.4 execute file, which fixes some bugs and enables 

Model rendering in the 3d view port. ( Note Hammer 3.4 needs to be installed first )

Hammer 3.4 - Valves Official Halflife Map editor.

Zoner tools 1.7 - New Compiler executes, Use these instead of the provided Q tools which some with Hammer.

XP Cagey Compile Tools - Modified Version of the Zoner tools, More designed for Natural-Selection.

Wally - Wad format based Texture maker/Editor, Plus you can create spray logos.

SPRview - Sprite File viewing utility.

Terragen - Sky Rendering package, ( tip : If you intend to render your own skies be sure to set the zoom to 1 )

WintExtract - Wad extracting program, Can take compiled textures from a .BSP and convert to .WAD useful if you lost your wadfile.

Batch Compiler - Graphical User interface for compiling.