There is a set of command line tools called Qeu listed here:
http://www.tldp.org/HOWTO/html_single/Quake-HOWTO/
ctrl-f for QEU
They are something you have to compile from source with the provided Makefile. If this is not totally strange to you, you could try them. There are two caveats, though.
As provided, the makefile is for DOS systems. To use in on Linux, you have to comment away this line as follows (# is the comment char you need to add):
#all.dos: $(PROGS.DOS)
A worse caveat is that the code apparently only works on 32-bit systems. It has some type definitions that assume 32-bit word size and hence it fails on a 64-bit system because it reads the wrong amount of data when examining a WAD file.
However, this can be worked around by using the -m32 flag to the C compiler and making sure you have the required C libraries for compiling 32-bit code. You have to install a suitable package, like libc6-dev-i386 on an Debian/Ubuntu system. (This is just if you use a 64-bit system. Ignore this step if you have a 32-bit environment.)
For reference, here is a paste of the modified Makefile that worked for me:
http://pastebin.com/PKzbcTvF
And here is just the diff if you prefer that instead:
29c29
< CFLAGS = -O2 -ansi -Wall
---
> CFLAGS = -O2 -ansi -Wall -m32
66c66
< all.dos: $(PROGS.DOS)
---
> #all.dos: $(PROGS.DOS)
Please ask follow-up questions if I didn't explain something clearly or you can't make the programs work for other reasons. Also, I didn't know how much programming experience to assume, so apologies if there was too much unnecessary explanation :)
Based on very little testing, I got these utilities to work on my 64 bit Linux system with these little tweaks. The relevant tools for extracting and constructing wad files are unwad2 and rewad2, which I specifically tested.