sodcha0s- installing apps on a seperate partition when running 1 single OS works sometimes, mainly because no other OS is dependant on those files or their location, but dual boot is different.
When dual booting the FAQs suggest that you could install applications once by running the install program within each OS and installing the application to the same location. Effectively installing one copy over the other, so both OS's know where to find the single install.
Problems with this approach
The problem with this is when you remove the program for some reason, like say to upgrade from Office 97 to Office 2000. You will run the uninstaller program from one of the OS's, which will work successfully. Then you go and run the uninstaller program in the second OS and it doesn't work because the uninstaller file doesn't exist (you just removed it from in the other OS) and the program doesn't exist. So you then go and put in the installation CD and try and run the uninstaller program from there, but that doesn't work because the program can't find anything to uninstall (it needs to see the entire program to restore the registry), and it needs the uninstaller application that should be on the computer to properly restore your registry and system.
Worse yet some programs, like Antivirus or Systemworks, won't let you reinstall the program until the previous version is removed(because the installer program can see in your registry that the previous version has not yet been uninstalled) , but you can't remove the previous version in the second OS (as stated above). So what do you do then? You have the program uninstalled from the computer and uninstalled from the first OS, but the second one can't use it, can't reinstall it, and can't uninstall it.
Keeping seperate copies (space permitting) of most applications is ok and keeps the management of each OS's available applications simple.
The other alternative
If you really only want to have to install the applications once, then you need a third partition (OS 1 on c:, OS 2 on d:, and applications on e

and a backup program like Norton Ghost. Then you would do exactly as the FAQ's suggest. Go into one of the OS's (like the one on c

and install the program on the e: drive. Then go into the other OS (the one on d

and install the program to the e: drive, over the install you just did from c:.
Then each time you go to remove/upgrade a program, Ghost the e: drive before you do anything. After you Ghost, remove the program from within the OS on c:. Then reload/restore the Ghost you just made of the e: drive. This will effectively put the program, and all your other programs back on the e: drive (like before the uninstall, except c: won't know its there), so the second OS has all the required files to successfully uninstall the application. Then uninstall from the OS on d:, which will now work successfully.
The alternative takes atleast 1 hour for every install/uninstall/upgrade of an application, as you have to make a Ghost, uninstall the application from c:, reload the Ghost and uninstall the application from d:, then install the new application within each OS. If you go with the original suggestion of keeping everything seperate, you uninstall two times and install two times, no 60 minuets of Ghosting required.
The only time you should have to spend more than 60 minuets to install/uninstall something (when keeping them seperate) is when you reinstall the OS, and since you would need Ghost for the second alternative, why not just get it anyway and create backups of the installs, and then you will almost never have to reinstall from scratch.