Most people come to Wakatobi hoping to leave with good shots of pygmy seahorses. There are five Hippocampus denise pygmies on two separate fans in the 2nd Gully, and according to Espen, up to three species can be found on the house reef. These are most easily photographed in the early morning before the "Wakatobi river" starts running (the current can be quite strong along the house reef). I quite enjoyed watching them flit about on their host gorgonians. They actually move around a lot, which is not something I had expected.
On trips out to more remote reefs, Hippocampus bargibanti pygmy seahorses can often be found. They are easier to photograph because they are the largest of the pygmies (a 100mm macro capable of 1:1, plus a diopter is sufficient). Most of us were very careful when photographing them, but I did see one photographer do some bad things (he had problems with bouyancy control, raked the fan with his strobes -- twice, and kept exhaling so that his bubbles went through the gorgonian -- where another pygmy was situated). I understand that accidents do happen; I am by no means innocent when it comes to damage to the reef. But it angers me to see people doing things that could be avoided through better diving skills, or through basic common sense. He had been pulled out of the gorgonian once already by the dive master, but went right back in after she left.
At Lorenzo's Reef is a rare, white pygmy seahorse, which I didn't get to see.
We also found a halemida ghost pipefish hiding in macro algae bearing the same name. The pipefish sat very still, hoping that we wouldn't be able to detect it, camouflaged among its surroundings. We also saw worm-like mushroom coral pipefish at Barracuda. They are in about 70-80' of water, hiding in a few large mushroom corals on the sandy bottom.