Appleseed is a manga from the 80s that got an OVA in 88. It was relaunched in 2004 with a film that got a 2007 sequel (Ex Machine) and 'Appleseed XIII' is a 2011 relaunch.
In the OVA, the female protagonist Deunan Knute has a scene 36 minutes in where she is sitting barefoot while cleaning her pistol.
Later a robot breaks into their apartment and kidnaps Hitomi who was sleeping barefoot:
Later the police officer dude has a flashback of when he is abducted by the police and strapped to a table. Then it returns to the present moment where he has Hitomi barefoot in a cell.
After the van she is locked in is shot down, the police officer pilots a mecha and carries her off again while busting up police bots.
After Briareos, Hitomi and the police apprehend Deunan, she is being looked after in a medical facility (being out for over 8 hours). Hitomi gets close, wondering if they gave her too much sedative. It turns out Deunan had awoken and faked being asleep, and suddenly jumped up. She is barefoot (except for some wrappings) and her feet are seen as she does a handspring off the table, backflipping behind Hitomi.
When Deunan gets angry at Hitomi's birthday party, she storms out and trips on the high heels she (a rarity) dressed up in for the occasion. She pulls them off and walks the rest of the way barefoot.
In "The End of Eden", when Deunan visits Hitomi's house, Hitomi eventually sits barefoot on the bed.
At the start of episode 2, Deunan is seen tossing and turning in bed while she dreams about a battle that occurred at the end of the previous episode.'
Deunan is seen chilling barefoot with Hitomi and a bioroid scientist friend (original XIII char) complaining about Briareos spying on her.