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I was thinking about setting up a five gallon fish only tank and was looking for suggestions for fish/inverts to go in it. I would like to have the option of eventually turning it into a nano-reef, so I would prefer any suggestions be reef safe.

A nano reef is exactly that, a reef. It does not necessarily mean a fish tank.

I'd putting nothing more than a small Goby in the tank. Outside of that not many fish if any can live their entire life in a 5 gallon tank.

I really like Hi-Fin gobies w/ Candy stripe pistols. It's an awesome combo and both stay very small. They would be great in a 5ga, and both are reef safe.

Yea, I've got a Hi Fin and Pistol shrimp, great combo, very intresting too. I wouldn't put them in a Fish Only tank they, they will defentinally need some LR to hide under, as well as a sand substrate with some coral rubble to help strenghten their home.

How much live rock would I need for those two? I was planning on sand as a substrate. I know that since the tank is small, I can only have 1-3 fish. Also, the reading I've been doing seems to indicate that a protein skimmer would not be worth the investment. Is this correct?

In a 5 gallon, you can really only keep one fish. If you got the Goby and shrimp, thats all I would keep. Especially because in that size tank, if another fish was present they likely wouldn't come out, assuming the fish was any sort of an aggressive feeder or fast swimmer.

The sand will need to be at least 2" deep, maybe even 3. That is where they live, so they need plenty of room. They have an elaborate system of tunnels. I know my pistol shrimp has caves from one side of my 75 to the other. He doesn't always use all exits and stuff, but often makes appearences on other sides of the tank.

You could probably easily fit 8-10 opounds of LR in the tank. I'd look for one or two really nice small looking pieces.

If ti was me, I would use Red Sea's Reef base for sand and do 2". I'd then get the measurements of my tank and find one 5-6lb peice of nice looking live rock that will fit inside.

With a pair like that, I would make them the only inhabitants. They will be seen a lot more often if this is the case.

Those sound like some great ideas. Is there anything in particular that I need to watch out for, any specific dangers unique to a small setup?

Water quality can go bad quickly. You need to be much more diligant with tank maintence. Top offs several times a day in some cases.