It might be more helpful if you list what files you are seeing. Perhaps you might check to see if you have the Klez virus which creates a different randomly named file that runs at each boot. For a free virus scan if you don't have anti-virus installed go to:
http://housecall.antivirus.com/pc_housecall/
Their scan also fixed the Klez on one of my client's PC's this week.
That aside, the only things that you need if your Windows 98 is a home program is:
Explorer (this -is- Windows)
Systray (this is the tray by the time, lower right in task bar)
Nothing else -needs- to be running although installing various programs including some hardware will cause other programs to run at Start. Check what's in Start, Programs, Startup and remove Find Fast, MS Office (not the shortcut bar), real player, etc. Right click on any icon in the systray to see if it has a context menu allowing you to exit it.
Since I just saw this, do the virus check first...
HTH.