Ok, here we go: get Milkshape 3D, decompile the model you want to modify (there's a built in decompiler for HL models in Milkshape), import the .smd files that make up the parts of the model (one at a time), select a different skin for them (in the right panel, third tab, select the material from the list, click on the button which caption is the name of the texture currently used for that material, select your new skin), then export as a new .smd under a different name.
Then, in the .qc file, fill in these new .smd's as options in the bodygroups. For example, take a look at the hgrunt's .qc file (you'll get this file after decompiling a model, it's necessary for compiling one) and you'll be able to figure out how the system works.
Once all that is done, compile (again, can be done from within Milkshape) and in Hammer, add the 'body' key and a value to select one of the combinations. You can always check in the model viewer if there are more options for the body groups, of course.
I'll assume this isn't a very easy guide, but if you're a fast learner, it should be enough to get you going in the right direction.
Lastly, I need to get some sleep, hence the quick info. See ya.