free rtos file system arm
There will probably be no "out-of-the-box" OS you can use.
The architecture you need so support is important (x86, ARM, PPC, MIPS, ...)
There are some open source RTOS-ses available that support multiple architectures.
eCOS and RTEMS are both OS-ses which support POSIX and File system, up to a certain degree,...
USB is a different story! Do you want USB host, device or On-the-Go.
In the case of USB Host: What kind of devices do you want to support, ... .
In the case of USB Device: What type of device do you want to develop, ...
My advice:
When you're not sure what you want to support and have the CPU/Memory, just go for Linux! Stay away from Windows CE when you're a small player!!! When Microsoft has a new version, you have to move to the new version to get any support. This means that you have to re-port your BSP (Board support package), ... .
Regards,
Antharax