PureSync is a free to use tool which lets you take automatic backups when ever you insert your pen drive on your computer, it lets you do the backup of the pen drive contents just like any professional backup program would do.
It lets you take incremental backup, as you can specify the backup settings when a file is modified, when a new folder is found and you can also schedulethe backup anytime.
But mainly it allows you to take incremental backup of your pen drive contents when ever its connected to your computer which is not provided by any free application at this time.