I stumbled into a set of resources which cover a range of embedded topics at useful levels of technical detail:
http://www.eeherald.com/section/design-guide/index.html
It includes a section of "On line Courses" on embedded systems and most common interface 'standards' including USB, I2C, SPI, CAN, LIN, Serial, and RS232. The sections I've skimmed seem to give reasonable coverage. There are also section on 'IEEE 802' local area and wide area networking standards.
USB is covered in
http://www.eeherald.com/section/design-guide/esmod14.html
I have not yet read it in detail, but it reads as good coverage of USB 2.0 basics.
These won't replace the manufacturers manuals (e.g. ST Micros STM32F RM0008), but it covers a lot of technical detail, and it looks pretty good. Maybe enough to understand before looking at code and RM0008.
Ideal Holiday Weekend reading :-)
(full disclosure: I am not a member of the LeafLabs staff)