There was a similar thread on this awhile back, so I just copy/pasted my reply from there, with some modifications for new additions and deletions.
Snakes ...
Malcolm - Mandarin ratsnake (Firefly themed)
Inara - Mandarin ratsnake (Firefly themed)
Atari - Thai Bamboo ratsnake (was before we started the Firefly theme and it just popped into my head and I liked the sound of it)
Serenity - Thai Bamboo ratsnake (Firefly themed)
River - Thai Bamboo ratsnake (Firefly themed)
Vera - Broad Banded ratsnake (Firefly themed)
Jayne - Broad Banded ratsnake (Firefly themed)
Zoë - Brazilian Rainbow boa (Firefly themed)
Wash - Brazilian Rainbow boa (Firefly themed)
Kaylee - Brazilian Rainbow boa (Firefly themed)
Simon - Brazilian Rainbow boa (Firefly themed) passed away last month :-(
Niska - Tricolor Hognose (Firefly themed)
Atticus - Western Hognose (book series themed)
Kittaning - Albino Western Hognose (same book series as above)
Indigo - African House snake (same book series as above)
Ukiah - African House snake (same book series as above)
Max - Tessera corn (same book series as above)
Tavia - Classic corn (was reading a bunch of books about the Roman Empire, it's short for Octavia but not for any particular character)
Vash - Phantom corn (based on two different book characters, one a dragon, the other a spy)
Stormy - Phantom corn (Just popped into my head and seemed to fit her)
Fiona - Honey corn (based on the Burn Notice character and a good fit for her personality)
Rhiannon - Caramel Motley, named by previous owner.
Esme - Rosy boa (my Mom named her, based on an old movie, I think)
Sebastian - Rosy boa (based on a book series character)
Emma - Rosy boa (daughter to the two above, just popped into my head)
Smaug - Honduran milk (one of my husband's first two snakes and named for the Lord of the Rings dragon)
Viserion - Albino Checkered Garter (my husband's other first snake, named for a dragon in the Ice and Fire book series)
Zuko - Amazon Tree boa. (ATLA themed)
Mai - Amazon Tree boa. (ATLA themed)
Sokka - Yunnan Mountain ratsnake (ATLA themed)
Iroh - Green Tree Python (ATLA themed)
I think that's all the named snakes ...
Almost settled on names for these but not sure they are going to stick just yet. These are all in the Firefly theme but there are a few other names we could use in that theme instead.
Badger - Charcoal Tessera male corn snake
Persephone - Charcoal Tessera female corn snake
Monty - Male Ghost San Felipe Rosy boa
Bridget - Female Ghost San Felipe Rosy boa
Geckos ...
Miami - Crested gecko (don't remember how he ended up named that but it set the theme for the rest of the cresteds)
Cairo - Crested gecko (she was named that by the person I got her from and it fit with the theme I had going on)
Luxor - Crested gecko (I bought him with the intent to pair with Cairo, so found a town I liked the name of in Egypt to name him)
Sierra - Crested gecko
Gizmo - Gargoyle gecko (took about a year to come up with but it set the theme for the rest)
Gadget - Gargoyle gecko
Gauge - Gargoyle gecko
Glitch - Gargoyle gecko
Box Turtles
Pell - Female, name from the same book series that two of our cats are named in.
Dag - Male, same as above.
Plus 2 GTPs that are unsexed and have names picked out for each if they are males or females but need to know which they are first ...