Hmmm, it looks like I may need to wait a few months before starting in on the Visitors arc - one of the recently announced DLC products deals with the mothership.... More critters, more weapons, and perhaps some backstory to fill in the gaps.
Makes it hard in one sense, the Darkened Tunnels arc ties in with the Visitors in a couple of places.
Missions that deal with the aliens that have appeared (dead, for the most part) in Fallout have titles along the lines of 'Just Visiting', 'Unwelcome Visitor', and 'Visiting Relatives' (or, 'What Do You Do When Your Relatives Pop In For a Visit, and It Turns Out That They Are Not Entirely Human?'
The plots dealing with Disney World have titles mangled from Disney movies and attractions. My favorite is the one that started me on this path - 'Walt Disney on Ice!'
The ones dealing with Gibsonton use circus, carnival, and especially freakshow references.
Feral Ghoul packs
Night Ghoul packs
Sand Lurks (Thanks to gaghiel42 for informing me of the Mole Crabs)
Crocogators - alligators bigger than a Nile Crocodile.
Doombats (name almost certain to change) humongous flying foxes with a potent sonic attack
Doodlebugs/Giant Ant Lions - trap building ambush predators.
And something very much akin to Green Slime from D&D.
Various and sundry carnivorous plants in the Everglades.
Pirates (water traveling Raiders).
Raiders (land traveling Pirates)
Wanamingo, umm, you know, umm, those, umm, things
The Auld Grump