I suspect this is because you are using vmware Server--it must have (slightly) different makefiles. There are a couple of things you can try. First try uninstalling/reinstalling vmware (to make sure everything is "pristine") and then applying the patch again. I'm not sure if there are any patches specifically for VMware Server (can anyone confirm this??) Note, you don't have to explicitly run "patch - (blah)." The sh script should do that for you.
This probably isn't what you want to here, although for now a workaround might be to use VMPlayer. If you need to create virtual machines there is a tutorial at
www.easyvmx.com (it'll do it for you, actually). You can still install vmware tools into the guest OS, you just need to extract them from your server installation. I did this before, and honestly can't remember how.
You will need the "bundle" version, preferably 2.5.x -- the earlier ones probably won't patch. You should be able to do, for example
chmod +x VMware-Player-2.5.2-156735.x86_64.bundle
./VMware-Player-2.5.2-156735.x86_64.bundle (stuff gets installed with a GUI here)
./vmware-6.5.2-modules-2.6.29-fix.patch
If all goes well,
mv /usr/lib/vmware/modules/binary /usr/lib/vmware/modules/binary.bak
vmware-modconfig --console --install-all
cd /etc/init.d
./vmware restart
Then you should be able to launch vmplayer as an ordinary user. Hope this helps.