It depends on what you're trying to do. If you're making skins, textures, etc., you'll need a good program for that (not my area of expertise, but I've heard Photoshop is good). If you're making models, animations (beyond simple shaders), etc., and you're rich, hey, go for studio. If not, there's supposed to be a good shareware model program out there (I can't remember the name of it) that can be set up with any game if the developer's write a converter for it.
If you're making maps, you'll need a MOHAA version of GtkRadiant, which is not available yet. If you have Wolfenstein, you can download the GtkRadiant tool for that and start playing with it to get used to it. The docs that come with it will tell you how ot use it, what the items in a quake map are, placing them, etc.
For any type of modding, you'll also need a plain text editor to write the tikis, urcs, shaders, etc., winzip (if you don't have Windows XP) to pak and unpak files, and (if you're really into it) a specialized text editor for scripting. Plus lots of little utils (text / file searching, etc., etc.,).
If you're looking to do a conversion or some type of in depth modding, you'll need a C++ compiler and the source code (which I doubt we'll ever see).
And one **** of a lot of patience.
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"If your philosophy does not produce corn, I don't want to hear about it." - Red Bear