Fish
Earthwatch: Manta rays at Ningaloo Reef, WA
Ecocean: whale shark research, WA
Corals and others marine invertebrates (and sometimes fish as well)
Earthwatch: Recovery of the Great Barrier Reef (Magnetic Island, Queensland)
GBRMPA: Eye on the Reef monitoring
Coralwatch (based at University of Queensland but involving citizen scientists): Monitoring health of coral reefs
Fluker posts: monitoring reef conditions and effects of storms etc.
Land invertebrates (butterflies, other insects, spiders, earthworms etc.)