One of the great aspects of modern USB flash drives is their flexibility. In the past, you needed an optical disc in order to either install and/or run a live operating system. Now that is no longer the case with tools such as Universal Boot Loader and Unetbootin. These tools automatically write the contents of a downloaded ISO to the USB flash drive and also allow write an MBR to them which will allow them to become bootable on modern machines.
http://www.pendrivelinux.com/install-knoppix-6-to-a-usb-flash-drive-in-windows/
http://unetbootin.sourceforge.net/
The following allows multiple operating systems to be booted from the same USB flash drive.
http://www.pendrivelinux.com/yumi-multiboot-usb-creator/
As you can see manual setup of a USB disk can be rather tedious. Hence, it is advisable to use the above when required and only use the resort to manual configuration when there is a very specific need to do so.
http://www.linuxjournal.com/content/dual-boot-opensuse-usb-stick-installer
The following demonstrates that you can boot both Windows (BartPE Recovery Environment) as well as a Linux from the same USB flash drive provided you have used the correct software.
http://www.irongeek.com/i.php?page=security/dual-boot-slax-linux-bartpe-windows-usb
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