Assembly's too high-level :) In my school's sophomore year, CS majors are required to implement a CPU on an FPGA; the instruction set, CPU architecture, everything are up to the student groups to design and implement. At the end of the class, all the student processors are compared w.r.t. size and speed of execution of various simple programs. Our group had a guy that wrote an assembler for our ISA, but most of the groups just wrote their programs in raw machine code, using a hex editor.

Really, nothing teaches low-level programming better than starting with gates and building your way up to programs. The sequel to that class teaches how to deal with pipelining, CPU caches, and multiple-execution chips like the TI DSPs, so after you design your processor, you get to see how real CPUs work. It's really fun, actually.