The wad and sprite formats have already been documented by others (most notably by Yuraj), and if you're a bit familiar with the HL modding scene then it isn't hard to find source code that deals with these formats, so parsing was actually one of the easier parts. Figuring out how to convert true-color images to 256 colors without too much quality loss was much harder.
If you're interested, here's how I'm making palettes: https://github.com/pwitvoet/wadmaker/blob/master/Shared/Colo... . It starts with creating a color histogram (the 'frequency list'), and then it treats these colors as 3D points within a 256x256x256 'RGB cube'. It calculates the bounding box for these colors and then splits this box along the longest edge. It then takes the box with the most colors and splits it up, and repeats that process until it has created 256 boxes. Ideally, these boxes will all be fairly small, which means that they contain very similar colors. A palette can then be created by taking the average color of each box (weighted by color frequency). When combined with dithering this produces quite reasonable results: https://raw.githubusercontent.com/pwitvoet/wadmaker/master/d... (but clearly there is still room for improvement!)