Is there a boot floppy or a boot manager like smartbootmanager (btmgr.sourceforge.net) to allow booting to a floppy disk as usual, but then being able to boot from usb - not just look at the files but to boot from it using the usb drive's boot sector - so I can run linux from it.

PTS DOS has a built in Boot Manager, wether or not this is able to be run from floppy I am not sure... http://www.phystechsoft.com/ptsdos/index.htm

There is a more basic question that has to be answered. Does the OS you want to run have a boot strap loader program that will load the OS files from a USB device and does it have system drivers that allow it to run from a USB device? If yes, then it is only an issue of putting the boot strap loader onto a diskette and running it at the proper loacation in memory. If windows has such a loader, you could boot and run it off of a USB device this way. However, doing anything with the USB interface like this requires a quite large device driver to access the USB interface. Not something normally done with a bootstrap loader. If you build a boot diskette that can access the USB device, it could load the OS's USB bootstrap loader and run it.