Well, I've fixed the speed issues with using GLSL (it's now just as fast as ARB shaders for the ones that actually work correctly) and gotten a few other things to work correctly. However, I'm still having issues with certain pixel/vertex shader combinations. Ohsix caught on that it may have to do with sampler limits on graphics cards and how sampling/textures are handled different in GLSL that with ARB. I'm not sure at the moment and could use some help.
http://cmhousing.net/wine/glsl_hack6.diff is the diff against the most recent git tree. There are still some ugly hacks lying around in there. Note that I've separated out most of the GLSL functions into a new file "glsl_shader.c". Once again, to use GLSL instead of ARB shaders, you'll have to apply this patch, have a graphics card that's capable of GLSL, and add the following case senstive registry key: HKCU\Software\Wine\Direct3D\UseGLSL = "enabled" (String value)