You can label the partitions on the flash drives with identifying labels if you have the right partitioning tools. For example, I have two flash drives each having one partition. Using Acronis Disk Director, I was able to give each partition a unique label, one "Backup" and the other "Data". Every time I insert the "Backup" flash drive, it mounts on /media/Backup and when I insert the "Data" flash drive it mounts on /media/Data. In general, once you label a partition on and external usb mass storage device, that partition will always be mounted on /media/<partition label>.
I know Partition Magic is capable of labeling FAT32 partitions as well. For ext2 and ext3 partitions, you can label them within linux using the e2label command:
# e2label <device file> <label name>
But I'm not familiar with any native linux tools that allow you to label FAT32 which is the way most flash drives come formatted. I think there may be a way of doing this using mtools but I'm not really up on that.