Scott,
I GHOSTED everything including the applications/programs. But I usually leave out the personal/user files and let the backup program do that job for me.
If my system crashed for whatever reason, all I have to do is REFORMAT my hard disk - that's right REFORMAT then use GHOST to restore all the OS and programs that I saved previously - no need to reload programs, drivers, etc. After that, I use the backup software to restore my personal files. I usually put all my personal files in ONE directory like MyDocuments so it's easy to backup.
This strategy has worked for me since my job requires me to use Win98 and as you know that system is prone to problems and from time to time I have to reload the software.