I think I read once that they served to cool the on-board computer systems, but I'm not sure.
It's for keeping the boundary layer flow from entering the intake, it's called a splitter plate. I think it's done to prevent turbulence inside the turbine (prevent compressor stall) and to make sure the intake doesn't ingest slow air, to maximize efficiency.
EDIT: I'd just finished writing out my own answer when I stumbled across this answer to a different question, which nevertheless explains the function of the small intake in greater detail. I've included my answer below anyway.
A couple of people have mentioned the splitter plate, but failed to address the smaller intake set between it and the fuselage. It's very difficult to find any references to this in particular, but my first instinct was that it's probably to do with either engine cooling (Concorde has additional intakes beneath the engines for this purpose) or engine bleed air.
After a bit of reading I resorted to Wikipedia, and found the passage below:
... the Hornet uses bleed-air vents on the inboard surface of the engine air intake ducts to slow and reduce the amount of air reaching the engine.
So it seems to be a simple intake for bleed air which has the additional effect of slowing the air entering into the main intake. Incidentally, this bleed air is redirected to a slots just above over the wing, to improve the performance of the aircraft.
The intake is for the primary heat exchanger. secondary is on the other side, Same location. The ambient air flows across a large rectangular heat exchanger. Basically a air to air radiator for the Bleed air system used for most functions on the F/A-18. Air conditioning, Wave guide pressurization, cabin pressure, avionics cooling, Gun,Etc. It cuts the air temperature in half and water is sprayed on the face of the heat exchangers that is extracted in the cooling process. Aids in cooling especially while sitting on the deck at idle. Otherwise you get a AVAIR hot code. The ACACS system has a water separator in it. That's where the water comes from. The Spent air and water exits on top of the aircraft. Basically without this system the Bird wont fly! If you ever see a F/A-18C throttle up on the deck you will see the water exit on top. It appears to be smoke but it is a water mist. I hope that answers some of the questions.
As suggested above it not an intake but rather a aerodynamic plate that keeps the boundary layer out of the engine. This is normally required for supersonic flight since the engines have to carefully manage the shock waves entering the engine. Most engine designs are not capable of operating under supersonic conditions and require that the inlet is carefully designed to create a series of shockwaves that slow down the air to an appropriate Mach number before it reaches the compressor.