For inter-IC interfaces, AMBA [1] and Wishbone [2] are open standards for connecting various sections of a chip --bridge between cpu, i/o bits, etc. External interfaces are also pretty open. A lot of FPGAs have dedicated logic for talking with a PCI bus, I2C bus, etc. Unless you're doing something extremely interesting and specialized, hardware's pretty open as is.
[1] https://en.wikipedia.org/wiki/Advanced_Microcontroller_Bus_A...