Your problem might lie in your Virtual Memory settings. Rightclick My Computer, thenProperties>Performance. Click Virtual Memeory, then select Let me specify my own v.m. settings. You'll then see the location and size of your swap file. Specify the same value for Minimum and Maximum size, so Win98 won't spend so much time resizing the file. A good rule of thumb is roughly 2 1/2 times your installed RAM, i.e. 16mbRAM, 40MB swap file.
Also, you have a Virtual Cache. Sometimes it can grow too large, filling up your memory.
Open System.ini in Notepad.
Add the following two lines to [vcache] section(add the section if its not there):
MinfileCache=0
MaxFileCache=16384
That of course is assuming you have at least 64MB of RAM.
You can also help yourself greatly by reducing the amount of stuff that loads at Startup. Run msconfig and open Start, and see what is loading that you don't immediately need. Some careful pruning here can save a load of resources.