Personally, I really liked Pemba, as it is more African than Zanzibar, more wild and more authentic. Over here you really have to cover yourself up (no bare legs or shoulders), for, unlike its neighbour, this island does not see tourists often, as everything is expensive here and those who seek to laze on the beach will be disappointed.
There is a lot of mangrove, one must take a boat or improbable dirt tracks to get to beaches (Missali Island is exceptional for snorkeling)... That is exactly what I liked! When you arrive at the northern tip of the island you feel as if you are at the end of the world, on an empty, windswept beach. Lots of divers come to explore the sea bed here.
The highlight was Ngezi forest, where I went on a lovely daytime walk with a park guide. Here I saw amazing flying-fox, the biggest bats in the world! They hang from the trees by the dozen, which is very impressive (however, they are totally harmless). I would have loved to have seen them active at nightfall (they sleep in the daytime).
Pemba's capital, Chake Chake is also a highlight of the visit, for the market and the small museum, definitely interesting even if it isn't much to look at on the outside.