Hornbills and toucans.
Swifts and swallows.
Lots of marsupials and the equivalent ecological matches within placentals (wombat/badger, numbat/anteater, devil/wolverine, marsupial mole/mole, many smaller marsupials/rodents, etc)
Storks and cranes.
Tuataras and lizards.
Moonrat and solenodons (tough they're more or less related, but moonrat is a hedgehog). Maybe better moonrat with Virginia opossum.
Buttonquails and quails.
Antlions and dragonflies.
Hatchet herrings (Pristigaster spp) and hatchetfishes (Gasteropelecidae)
Alcids and penguins.
Horseshoe crabs and decapod crustaceans.
Grass lizard (a kind of girdled lizard!) and more typical legless lizards such as anguids.
Sandgrouses and partridges.
Sturgeons and sharks.
Caecilians and earthworms.
Ricaniid planthoppers and moths.
Knifefishes (Apteronotidae, Gymnotidae) and knifefishes (Notopteridae)
Pangolins and armadillos (maybe a bit forced but..)
Brachiopods and bivalves.
Hummingbirds, sunbirds and honeycreepers.
Jellyfishes (Scyphozoa) and freshwater jellyfish (that is an hydrozoan).
Of course, all the circle of batesian mimics: a lot of beetles, flies, spiders, grasshoppers and more that mimics perfectly wasps, ants, velvet ants, lycid beetles, etc, as well as unrelated butterflies/moths that mimics perfectly toxic butterflies/moths (Hypolimnas misippus and Limenitis archippus with monarchs, Epicopeia and some zygaenid moths with swallowtails, Alcides agathyrsus and Papilio laglaizei, etc etc.. there are infinite)
Regarding extinct groups: nautilus and ammonites, phytosaurs and crocodylians, ichthyosaurus and dolphins, pliosauroid plesiosaurus and mosasaurs (the latter are actually related with snakes more than something else)