To avoid influencing myself, I've avoided every other post in the thread before making this post. I'll go back and read them right afterward.
Because of "Pinkamena Diane Pie", I actually did exactly this way back when — at least with the main gals and the CMC — and pissed off everyone in my RP by, uh, kinda pushing it on them all a bit hard.
Some of these names (but not all) follow one or more of the below conditions:
1. The regular pony name can be formed by trash-compacting the "full name" (the canon-ish "Pinkamena Diane Pie" fulfills this condition)
2. The name relies on an old "headcanon" that is no longer show-compatible
3. The family are country hicks so the middle name is some awkward thing like "Benevolence"
Twilight Sparkle: Dawn Athena Sparkle
Shining Armor: Sigurd Adonis Sparkle
I don't remember if the canon has any hint of this, but our Twilight Velvet was a classy romance novelist. Because of that, I used literary / mythology middle names for her children. Athena is the Greek goddess of wisdom, while Adonis is… basically the god of being a hunk.
Twilight is a parody of a Mary Sue, at least in terms of her character design, and Dawn is a good Mary Sue name. It is of course a more hopeful not-day-or-night cliché than "twilight" is and leans closer to the sun; Twilight has a more concrete relationship with Celestia than with Luna.
Sigurd is from Norse mythology. He was a big hunky dragonslayer. Shining Armor is not that far off from him, I think. (And they both start with an S.)
Rarity: Rachel Clarity Belle
Sweetie Belle: [???] Belle
I used to know this super cute gal in elementary school named Rachel. "Rachel Clarity" could be trash-compacted into "Rarity". She goes not use her country-as-hell surname because, if you didn't notice, she is kind of ashamed of her country roots (but not always.) Using "Clarity" as a middle name is, of course, a very country family thing to do.
I don't remember Sweetie Belle's "full name"; just that she's why the surname was Belle.
Applejack: Jasmine Constance Apple
Apple Bloom: Brooke Faith Apple
Big Macintosh: Maxwell [???] Apple
Granny Smith: Gruntilda [???] Apple
"Jack" is a very common nickname. You can use it regardless of what someone's actual name is, but "Jasmine" was the closest feminine name I could think of that wasn't PoS Jacqueline. Like with Rarity, middle names like "Constance" are pretty old-timey and/or rural. Constance, the word, is a pretty similar concept to trust or honesty.
BROOKE IS A SUPER CUTE NAME and vaguely sounds like Bloom, if you're drunk enough. "Faith" was basically just a random hick middle name as it is not needed for the inverse trash-compaction.
Granny is just short for Gruntilda… but I refuse to permit any other "human name" for Granny. I see nothing wrong with comparing Granny to the only other recognizable figure to bear that name in the last 30 years.
[we can obviously skip Pinkie because yeah]
Fluttershy: Florina [???] [Sher-something]
Trash compactor rule was in full swing here: the first draft of the name was Florina Terra Sherwood. That's three things that no pegasus would ever be named because they don't, as a daily life culture thing, know what flowers, earth, and wood are. The only reason is that the first syllables are FLO-TER-SHER. The Nordic Fluttershy.
Florina is a cute name for her, but the other stuff needs adjustment.
Rainbow Dash: Danielle [???] Rainbow
Scootaloo: Alfreda Bernadetta Lucchesi
I actually didn't name Rainbow Dash. Her player basically immediately picked that name as soon as he saw me naming characters, and I dared not get in the way. Dash's family was not revealed at the time and the player basically made all of them rainbow-haired jocks. This was all rather agreeable, I think.
Scootaloo's parents would not come home for the next 7+ years, so we all made up our own ideas. Mine was that she was actually from a rich noble family and absolutely despised being a "proper lady", so she never talked about her family, not even to shut Diamond Tiara up. So, I gave her the snottiest noblest name I possibly could. "Alfreda" is a pun on chicken alfredo due to the scootaloo chicken meme. Bernadetta is there solely because that is a terrible middle name she would hate. "Lucchesi" is a cool-sounding name from the -loo in Scootaloo. The slightly complicated idea there is she would've refused to answer to her first or middle name, forcing people to call her Miss Lucchesi or some such. This was soon shortened to Lu. She rode a scooter, so she became Scooter Lu. This was soon slurred to Scootaloo.
Celestia Aurora Pendragon
Luna Selene Pendragon
There is no bosser surname than PENDRAGON. It generally either means you are a dragon or one of your ancestors was. In our RP, I played Celestia, and she got so mad at her sister once that she turned into a bigass dragon (our Luna feared dragons) and perched outside in the cold and refused to move or turn back until Luna said she was sorry.
Aurora and Selene are just dawn and moon names in some mythos or another.
Gilda: Grizelda [something something]
In general, longer female names are more embarassing and lady-like, so I like to give them to tough girls the way big biker dudes are named stuff like Sally.
Gilda would have shortened her name during her school bully days. I didn't give her anything but a first name.