Alpine: My favourite is Ibex/Markhor. I sometimes add Gelada as well.
Boreal Forest: Moose/Triceratops, the only one I can leave unattended for long periods.
Desert: Camel/Oryx/Addax, also Tortoise/Fennec Fox.
Grassland: Bison/Wild Horse.
Savannah: ALL the herbivores. Limit it to that.
Scrub: Again, all the herbivores, as well as the Aardvark and Meerkat, go together. In fact, the first ME I built with AA was an Aardvark/Gerenuk/Meerkat/White Rhino exhibit.
Temperate Forest: What fits nicer than a Giant Panda/Red Panda exhibit? Well, I do think a Red Panda/Peafowl exhibit looks more real.
Tropical Rainforest: Bongo/Chimpanzee/Gorilla/Mandrill/Okapi/Pygmy Hippo, Gibbon/Javan Rhino/Orangutan and Styracosaurus/Tapir.
Tundra: Caribou/Musk Ox for the land exhibit, and Beluga/Narwhal for the marine exhibit.
Wetlands: Hippo/Flamingo/Buffalo.
Benthic: Whale Shark/Goblin Shark.
Coastal: I find that a Dolphin/Turtle/Otter mix works nicely, as does a Sea Lion/Manatee mix.
Pelagic: Pilot Whale/Leatherback Turtle. I did use the Blue Marlin twice, but on the third attempt, the Whales tried hunting them.
Reef: Now, I've never mixed anything here. I know lots of people mix the two animals of that biome, but don't the sharks eat the Mantas? Or are they too big?