TWT, or TOGoS Wad Tool, is a lump management tool, written in Ruby, that is primarily meant for command-line or batch compilation of WAD files. You don't actually need Ruby to run it, as a Windows EXE is included. As of version 3, TWT does not do any graphic or sound conversion. However, it is very good at moving raw lumps around, and it can be argued that, since ZDoom now natively supports PNGs for graphics and common sound files for music, lump conversion is hardly necessary anymore, anyway.
Here is an example TWT command which creates a wadfile including a README lump, a marked (between empty TX_START and TX_END lumps) set of lumps including whatever is in the directory textures or textures.wad, and all the maps in the maps directory (assuming TWT version 3.0.x):
twt -o wadfile.wad README=readme.txt m:TX_START tx/* m:TX_END maps/*.wad
You can also use twt to extract lumps:
twt -x readme.txt wadfile.wad/README
Or clean wad files:
twt -o new.wad old.wad
Download it from http://www.nuke24.net/projects/TWT/archives/
If you have questions/comments/bug reports about TWT, please add them to the /talk page as TOGoS looks at that sometimes.