When Virus Warning is enabled, the BIOS will flash a warning message whenever there's an attempt to access the boot sector or the partition table. You should leave this feature enabled if possible. Note that this only protects the boot sector and the partition table, not the entire hard disk.
However, this feature will cause problems with the installation of certain software. One good example is the installation routine of Win95/98. When enabled, this feature will cause Win95/98's installation routine to fail. Disable it before installing such software.
Also, many disk diagnostic utilities that access the boot sector can trigger the error message as well. You should first disable this option before using such utilities.
Finally, this feature is useless for hard disks that run on external controllers with their own BIOS. Boot sector viruses will bypass the system BIOS and write directly to such hard disks. Such controllers include SCSI controllers and UltraDMA 66 controllers.
Some motherboards will have their own rule-based anti-virus code (ChipAway) incorporated into the BIOS. Enabling it will provide additional anti-virus protection for the system as it will be able to detect boot viruses before they have a chance to infect the boot sector of the hard disk. Again, this is useless if the hard disk is on a separate controller with its own BIOS.