K.:
I have 2 kids ages 2 and 4. Both seemed to go through this (and the 2 year old is in it now!). It seems at this age they are cognitively developed enough to have fears. Fear of the dark is a big one, I didn't see this on the list but maybe you already do it: night light and/or light on at bedtime. The other one is "Monsters" or similar fear. With both our kids we had to do a "monster check" of the room before bedtime. We gave them a flashlight the together we would check for mosters...under the crib, in the closet, behind the door, etc. My son was also afraid of cars (driveway was under his window and car alarms/cars starting would scare him). He thought that the cars would get inside the house, when I explained that they were too big to get through the door he calmed down and eventually this wasn't an issue for him.
Take home message from all my blathering: you have to think outside the box to figure out the real trigger here. Then, depending on what it is, get creative to help them feel some "power' over the fear (if it is fear related). I have also heard of some filling a spray bottle with water and using this as "monster spray" to keep the monsters out at night.
Good luck! My 2 year old is scared of clowns on the ceiling! Not sure where that came from....I use the dust buster to "scare" it away-is working for now:)