This largely depends on the application you are installing. If it allows you to choose another install location then it should work from another folder (or drive, in your case). However, if the installer doesn't ask for an install path, there might be some references to the Program Files folder in the registry keys the program creates, or worse: hardcoded.
I would probably try it one app at a time. If some do not work from another drive then you'll likely have to install to C:\Program Files\
Note: You could also accomplish this more cleanly in Vista / Windows 7 using symbolic links.
EDIT: I just found this link, but I have never done this... try at your own risk:
Click Start -> Run (or Windows key +
R) Type regedit and click OK.
Scroll to the key: HKLM \ SOFTWARE \
Microsoft \ Windows \ CurrentVersion
On the right window, double click on
the key ProgramFilesDir and modify
data in this key by the new path for
the installation folder.
For example, enter the path D: \ Program Files, to change the partition
on which the facilities are.