I bought a couple different sizes of SMDs, some 2mm tower LEDs, and various sizes of fiber optics (.5mm, .75mm, 1mm) and just tried them all. I have decided to go with 1mm fiber optics attached to ultra-bright LEDs. I will be using some of the SMDs I picked up for the observation decks and the planetary sensor, so the purchase wasn't a complete waste. I really liked the look of the brightness/pattern cast on the registry from the 2mm tower LED, but it was just too damn big to even think about putting it in the space provided.
While 1mm is a bit larger than the scale floodlight openings, it's as small as I could go while still casting a decent pattern and a good amount of light. My personal preference is to have the lighting pattern cast on the saucer to be more accurate than the size of the hole the light is coming from. BTW, the trick where you hold a lighter kind of close to the end of the fiber and watching carefully until it just starts to melt for a make-shift lens works really well. I already have fiber optic holes drilled for the 3 bridge floods, registry, upper and lower cargo bays, shuttle bay, and interior pylon floods.
Note that in this pic, there is only a single LED active, and that is the only thing leaking thru windows, etc. Still waiting on it to warm up enough to airbrush my aluminum base coat, then I dive in on the wiring! Very excited.