Naaah, if you're getting into hardcore modelling and such, you want more than Milkshape...3dsMAX and Maxon 3D are excellent programs that are much more effective and more stable than MS3D IMO. They are expensive commercially but if you search enough you can often find enormous educational discounts for non-commercial usage, which is fine unless you want to release your mod commercially and charge for it.
You'll also want the HL SDK from the ERC, thats a must for any mod makers, and you want to get things like Kratisto's MDL Decompiler, and the utilities that come with the SDK like StudioMDL and some other programs.
As always, make sure you have the latest ZHLT and you should be good to go.