С(++) (unmanaged) really compiles to plain binary. Some OS-related stuff - are BIOS and OS function calls, they're different for each OS, but still binary.
1. Assembler compiles to pure binary, but, as strange as it gets, it is less optimized than C(++)
2. OS kernel, as well as bootloader, also written in C, so no problems here.
Java, Managed C++, and other .NET stuff, compiles into some pseudocode (MSIL in .NET), which makes it cross-OS and cross-platform, but requires local interpreter or translator to run.
