If you have a CD/DVD writer, you can write the files to a CD-R. If this is not an option, take out the HDD from he Win 98se machine and install it in the vista machine, if you have room. you might need to disconnect your CD/DVD drive in your vista machine to free up the EIDE ribbon cable.

option 3:
Win 98se can do USB, but not very well. And drivers are hard to come by for usb flash drives. Vista/XP/ win 2000 can handle them without needing a driver disk. Therefore you will need a new OS for the win 98se machine. How about linux, it can handle usb flash drives very well. My advice use Ubuntu linux, you don't need to install it, just get a boot CD. it boots the OS from the CD, does not install or format anything. Use that OS to copy the necessary files to the flash drive. This option requires you to have a cd burner or access to one, so not really saving any time.

http://www.ubuntu.com/

You did not give ne a lot of information about your setup. Like do you have a cd/dvd burner, any usb ports, any spare HDD, any external media storage. Do you have any burning software like nero. So pick which option that is viable.

You can also take your computer to best buy and have them back up the data on a CD/DVD disc for a price. Best Buy is not the only shop that does this type of service, check in your area.