Lara Croft can be a great character to pair with the Doctor. She's an adventurous archaeologist, and when combined with the Doctor's exploration of different planets and time periods, it can lead to some exciting treasure - hunting and mystery - solving adventures across different dimensions.
Sherlock Holmes is a popular choice. The contrast between the Doctor's time - traveling and otherworldly adventures and Sherlock's deductive reasoning on Earth - based mysteries can create some really engaging stories.
Superman is also often paired with the Doctor. You have the Doctor's intelligence and ability to manipulate time and space, and then Superman's superhuman strength and moral code. Their interactions can be used to explore themes of heroism and the greater good on a universal scale.
Hermione Granger and the Doctor are also often paired. Hermione's thirst for knowledge would be well - matched with the Doctor's vast knowledge of the universe. They could have long discussions about different forms of magic and science, and perhaps even collaborate on some sort of project that combines both.
In crossovers with other shonen series, characters like Luffy from One Piece can be paired with Ichigo. Their different personalities and power sets would create interesting dynamics. Luffy's carefree nature contrasted with Ichigo's more brooding side could lead to some humorous and action - packed adventures.
Rukia is a very popular character to pair with Renji in crossover fanfiction. Their long - standing relationship in the original series makes it interesting to see how they interact in different crossover scenarios. Ichigo is also popular. Given their rival - like relationship in the main story, in a crossover, they could end up as allies against a new common enemy.
The Daleks are often prominent in 'Time of the Doctor' fanfiction too. They are such a classic enemy of the Doctor, and their presence always adds tension. Fanfic writers might explore new ways the Daleks interact with the Doctor during this story or give them new motives.
Sonic is a very popular character to pair with Shadow. Their rivalry and yet potential for teamwork makes for great fanfiction. Tails is also often paired with Shadow. Tails' intelligence can complement Shadow's combat skills. And Knuckles is another one. His strength and connection to the Chaos Emeralds can create interesting storylines when paired with Shadow.
Well, of course, the Doctor is always a popular focus. But from Torchwood, Toshiko Sato is quite interesting. Her technological expertise could be very useful when combined with the Doctor's knowledge. She could also learn a great deal from him. Another character that can't be ignored is Martha Jones. Although she has her own story with the Doctor, when she gets involved with Torchwood in the fanfiction, her medical skills and her past experiences with the Doctor can create a whole new set of storylines and character relationships.
Luffy from One Piece is also a common pairing. Luffy's carefree and adventurous nature combined with Ichigo's more serious and duty - bound personality would lead to some really fun and unpredictable interactions. They could be on a quest in a crossover world, with Luffy's devil fruit powers and Ichigo's Soul Reaper abilities working together in strange and amazing ways.
The Road Runner could be an interesting character to pair with Rango. Their different styles of movement, with Rango being more of a swaggering walker and the Road Runner being super - fast, could create some really fun and comical interactions. Another great pairing would be with Shrek. The contrast between Shrek's ogre - like nature and Rango's lizard self would make for a great story of two misfits coming together.
The Doctor herself is always a very interesting character. Her intelligence, quirkiness and compassion make her a central focus. Her companions are also great. Yaz, for example, is often explored more deeply in fanfiction. Her growth from an ordinary police officer to a time - traveling adventurer is a fascinating arc. Then there's Ryan, with his dyspraxia, which can add an interesting layer to the stories as he overcomes challenges in different situations.
The Daleks are extremely memorable. Their menacing appearance and their single - minded goal of exterminating all non - Dalek life forms make them iconic villains in the series.