|If it's THE system.ini file you can restore a previous version. Start up the computer. Before the OS starts to load start tapping F8. A boot menu should come up. Choose 'safe mode, command prompt only'. At the c:\> prompt type scanreg/restore and enter. Choose a registry to restore with a date prior to you deleting that file.|
Scanreg/restore will restore the previous registry along with system.ini and win.ini.
Depending on what you actually deleted, the above may be all you need to do. If you actually need to do a reinstall, as Derek mentions, you should start off booting with the 98 cd or bootdisk and not the hard drive.
Real men don't use AntiVirus; they just reformat