Kara, Detroit Become Human.

I'm gonna cheat and give 3 I don't see mentioned

Red from Transistor
Miriam from Bloodstained: Ritual of the Night
Ajna from Indivisible

Two occur to me: Chell from the Portal games, and Lufia from Lufia and the Fortress of Doom. And both of those almost don't count.

I almost don't want to count Chell because she's almost not a character, but I've had quite a bit of fun playing as her.

Lufia is one of the rare SNES JRPGs not made by Squaresoft or Enix, it was published by Taito. Gameplay is similar to classic Final Fantasy, the story manages to be quite tragic. Lufia, the title character, is not the player character, Enter Your Name is the player character, and Lufia is a playable party member/his love interest/...well, play the game to find out. So there's reasons why I hesitate to call her a "protagonist."

I have to mention a fun thing that series did: Lufia 1 starts with a playable prologue/tutorial section where you play as some legendary heroes fighting an ultimate battle. Lufia 2 is a prequel, and it's the story of those legendary heroes, which ends with that same ultimate battle as the final boss. In Lufia 1, the heroes speak very formally. They sound stalwart and brave and a bit old fashioned, as legendary heroes should. In Lufia 2, we know these characters more as real people, and the dialog treads the exact same ground but it's much less formal, makes them sound less hypercompetent.

Probably April Ryan from the Longest Journey. She was clever, empathetic, funny, and grounded. She certainly had more than enough opportunity to get annoying over the many, many hours it takes to play that game but I found myself reading the journal that served as a story tracker just to see what she had to say about events. I genuinely missed her during Dreamfall. Though I had a few other favorite games with female protagonists that I loved (like Rynn from Drakan, Cate Archer in No One Lives Forever), it says something that decades later I still remember April's name, and her major character traits.

Books

Aloy from Horizon Zero Dawn.

She's beautiful.. and mean with a Banuk Powershot or Gravesinger's Lament bow.

Adalia from En Garde, or Tchia. (sidenote: the ukulele simulator in Tchia is pretty cool)

More people need to know about En Garde. The sheer joy of the game is infectious. You can stun enemies by putting a roast turkey on their heads, amongst other hilarity.

Maya Amano from the Persona 2 duology

"Let's think positive!"

if you know you know

Estelle, from Trails in the Sky.

She’s introduced as a bit of a cocky moron who constantly has to be wrangled by her more mature brother. But, there’s a slow development of competency where she starts to become decently sufficient at all the things her brother is good at, while he meanwhile lays bare some heavy emotional flaws - many of which Estelle excels at processing (call it a feminine trope, but it works).

Of note, all the rest of the Trails series have had male leads, and their pace of character development ground to a complete halt.

(edit: MARKDOWN FUCKED UP THE SPOILERS, readers beware)

Robin from Iconoclasts:

• Pacifist until the end (depending on the definition of "end"), despite the game's pixel aesthetic it tries to make it clear that murder is her last option;
• Altruistic, she goes out of her way to help people with complete disregard of her own safety;
• Doesn't talk much;
• Kind hearted, doesn't reject a well-intentioned yet spoiled acquaintance even though fucking up is his character arc and everyone hates him;
• Plot spoiler

  becomes friends with Jesus and goes with him back to heaven
• Ending spoiler

  fucking kills god, then fills Him with seeds (tbf all the poor guy did was pull up at the gas station and have strangers harass Him)
  • Plot spoiler

    she also fills Jesus' mom with seeds, I'm beginning to think she has a thing for the clergy

Heather Mason from Silent Hill 3

Angel fom Total Overdose

Shukran from Arabian Nights: Sabaku no Seirei Ou on the Super Famicom

Ifrit is a djinn who was once the king of the djinn. Then he was cursed and bound to a ring until he granted the wishes of 1000 people. He's granted wishes to 999 people when his ring comes into the possession of an orphan girl named Shukran. Over the years he's become bitter and cynical, and he just expects she's going to want gold or such, but instead, to his surprise and dismay, she wishes to bring peace to the land. And she means it. So Ifrit has to first set out to find and recruit the most powerful of his former djinn subjects, and since he can't stray far from the ring, Shukran has to come along.

She's far and away the weakest character in the game, but at every turn, when it's (eventually predictably) revealed that whichever djinn they're trying to recruit at the moment has a well-deserved grudge against Ifrit and no intention of helping him with anything, it's Shukran and her optimism, determination, honor and kindness that wins them over, and (after Shukran and Ifrit and their allies complete whatever trial or quest the djinn tasks them with) they end up swearing allegiance not to him, but to her. So while she herself remains ridiculously weak, she is very much the driving force behind the party. And over time she can summon more and more powerful djinn in battle, and they're decidedly not weak.