If you plan to install all your programs on another partition, I'd recommend setting the C: partition to 1.5 to 2GB for Win98.

Bear in mind that if Windows is shut down incorrectly or there's a power cut or some such event then the next time you boot Windows will run scandisk. Not a problem normally but if it's running in Thorough mode, it'll take absolutely forever to complete with a very large partition.
I know you can exit before it's finished but it's a good idea to let scandisk run it's course once in a while.