I'm running a 7 gal nano-reef right now as we speak!
It's been up for over a month, and everything's doing great. So, no, 5 or 6 gallons isn't too small - it's just NOT EASY!
It's not the best setup for a beginner, since if anything goes wrong, it'll go wrong in a big way. You also have to constantly check your levels and do water changes regularly (i do about 20-25% every week) if you're going to have fish.
However, don't let this discourage you - it's kind of overwhelming at first, but you get into the habit of it eventually.
I got a small tank that has a similar set-up to an eclipse, but it's set-up for salt water. The filtration's a bit different, and it came with white and actinic-blue 50/50 power compacts. But if you just want a clown fish, an eclipse set-up should be okay, like i said, just do the water changes.
I would definately suggest a LS substrate and some live rock (at least a 1:1 ratio rock:tank size) this will definately help you with the biological filtration. Then once everything is cycled and the levels are good, go ahead and add the clown and a few snails, and maybe even a coral if you can keep the water good.
Just to give you an idea, in my 7 gal i have about 3-4" LS, almost 10 lbs LR, a pulsating xenia, a trumpet coral, various mushrooms and polyps, an anemone crab, 3 astrea snails, a small brittle star, a catalina goby, a rainford goby, and a red firefish (yeah, i'm probably overstocked but everything's doing fine and my levels are good - plus i'm planning on upgrading as soon as i get a bigger place).
So, in short - yeah, 5 or 6 gal shuld be okay for a small clown
I'm sure people will have very different opinions on this though...