Characters and Fandoms
Kara Zor-El / Linda Lee / Supergirl - Supergirl (1984)
Dick Grayson / Nightwing - Batman / Nightwing comics. This version is a refugee from another dimension - See Five Dates Supergirl Didn't Enjoy…, and One She Did
Phoebe Halliwell - Charmed
Talking cats - Young Wizards series by Diane Duane - See Cat Chaser
Larry Fleinhardt - Numb3rs
Bruce Wayne / Batman - Batman Begins and sequels
Selina Kyle - Batman comics and the Cat Tales fanfic series by Chris Dee
Debra Morgan - Dexter TV series - see notes below
G. Callan, Kensi Blye, Sam Hanna, Hetty Lang - NCIS Los Angeles
Cybertronians - Transformers movies
Clark Kent / Kal-El / Superman - Superman Returns

Also Mentioned
Lois Lane, Jason - Superman Returns
Doctor Samantha Carter - Stargate SG-1
Doctor Harleen Quinzel a.k.a. Harley Quinn - Batman comics.
Oliver Queen - Arrow TV series
Thom Gemcity - Pen-name of Timothy McGee, NCIS
Abby Sciuto, Ziva David, Tony DiNozzo - NCIS
Jonathan Kent - Lois and Clark's second son, named for Clark's adoptive father, invented for Red Chief Protocol
Hancock - Hancock
Willow Rosenberg, Dawn Summers - Buffy the Vampire Slayer

Notes
"the kryptonite Luthor was selling on the black market when he couldn't con suckers into buying a fake" - See The Return

"Remember that thing with the robots in Wales? Or the kidnap attempt?" - See Jason and the Cybernauts and Red Chief Protocol

"a range of science toys for girls called Linda's Laboratory" - See The Return

In Five Dates Supergirl Didn't Enjoy… and One She Did Dick Greyson gave Bruce Wayne a list of criminals from his home universe, including several that were yet to commit any crimes in this universe. He monitors them and tries to steer them away from crime. He also has a list of heroes, including Oliver Queen, and for the purposes of this story intervened after it became clear that Queen was killing criminals.

"…the environmental report you wrote after talking to Poison Ivy?" - See The Return

"I doubt he killed fifty-five people." Oliver Queen's estimated body count in Arrow S1
http://www.comicbookresources.com/?page=article&id=50300

"The Bay Harbor thing? A few years ago? Gibbs' team caught him?" - see Give the Boys a Great Big Hand - which wasn't specifically set in the Supergirl Returns universe, but there's no reason why it couldn't be. Now imagine Harleen Quinzel as Dexter Morgan's new prison psychologist...

Give The Boys A Great Big Hand
On Twisting the Hellmouth - http://www.tthfanfic.org/Story-23164/MarcusRowland+Give+the+Boys+a+Great+Big+Hand.htm
On AO3 - http://archiveofourown.org/works/111816/chapters/155211


"…we met her at a crime scene, we were too busy dodging bullets to be tongue-tied." - see Adventures in House-Sitting

"it's Agent DiNozzo's wedding on Tuesday, he and Ziva are really hoping you'll be able to attend." - gratuitous fix-it for events in NCIS S13; Kara intervened and one result was that Tony and Ziva got back together.

The L.A. Tribune was the daily paper in the TV series Lou Grant.

The Ultra-Girl series was, of course, suggested by the current Supergirl TV series, and by Lois and Clark: The New Adventures of Superman, in which Lois Lane used the identity of Ultra-Woman when she briefly had super-powers. My inspiration for the John Henry series was numerous examples of white-washing in films, TV and book cover illustrations.

For story purposes the Transformers haven't been on Earth long; both groups landed at about the same time, and bought their fight with them.

Linda's contact with Dawn Summers and the supernatural is first mentioned in Yesterday's Ghost.

Marcus L. Rowland
Forgotten Futures, The Scientific Romance Role Playing Game