(October 2, 2017)
Terragen is a program for generating scenery. It's one of the most advanced tools a mapper could have in their toolbox, and it's perfect for generating 2D skyboxes. Everything about your scene can be configured, including terrain generation algorithm, terrain shape, terrain texture, cloud density and size, atmospheric conditions, sun conditions, hazing and light scattering, light decay, shadows, and water level.
This download of Terragen is the final freely-available version, version 0.9. The unregistered version can render scenes at a maximum size of 1280x960. This is more than enough for modding, however, as GoldSrc skies are locked at 256x256 per side, and Valve's default Half-Life 2 skies have a side size of 512x512.
Included in this copy of Terragen is a script for rendering out skyboxes. To use it, place it anywhere on your hard drive, position the camera in the 3D preview to match the location of your render and run "Execute script..." from the Terragen menu. Select the script and wait; six bitmaps will render out, which you can then convert to TGA or VTF and use in-game.