There are quite a few. One popular one is 'The Time-Traveling Witch' where Hermione gets transported to the Doctor Who universe and has amazing adventures.
Well, 'The Magic of the TARDIS' is a well-known crossover. It combines the magical world of Harry Potter with the adventures of the Doctor in really interesting ways. The characters' interactions and the plot twists make it a great read.
Another great one could be those crossovers with the 'Lord of the Rings' universe. In these fanfictions, Harry Potter might find himself in Middle - earth, facing new challenges and making alliances with characters like Frodo or Gandalf. The contrast between the magic systems of both worlds makes for an interesting read.
I'm not sure specifically which ones are the most popular. However, you can start by looking on fanfiction platforms like Archive of Our Own. There, you can search for 'fem Harry Potter gets knotted' and browse through the results. Some might have high ratings and a large number of reviews which could indicate their popularity.
You might find fanfictions where Fem Harry has adventures with characters from Doctor Who or where her magical abilities interact with the Doctor's time-traveling escapades.
A well-liked one is 'Time and Magic'. It weaves a tale where Harry and Hermione's presence brings a unique dynamic to the Doctor's travels, facing challenges and uncovering mysteries together.
Fem Harry herself is often a very popular character in these fanfictions. Her new take on the traditional Harry Potter role brings a fresh perspective. Hermione also remains popular as she is often Fem Harry's closest friend and ally. Viktor Krum is also a popular character as his relationship with Fem Harry can be explored in new and interesting ways in the context of the Goblet of Fire story.
One interesting 'Harry Potter is a doctor' fanfiction could be where he uses his magic in a new way to heal patients in the Muggle world. He might combine spells with modern medical knowledge. For example, he could use a spell to quickly diagnose an illness that normal Muggle doctors find difficult to detect.
One great Harry Potter crossover fanfiction is 'A Very Potter Musical' which combines the world of Harry Potter with a musical format. It has humorous takes on the characters and situations from the original series. Another one could be those crossovers with the 'Percy Jackson' series, where the magic of the two different mythologies interact in interesting ways. There are also some crossovers with 'Doctor Who' that take the TARDIS into the wizarding world and create unique adventures.
One popular fem Harry Potter as a Veela fanfiction might be 'Veela's Magic'. In it, the fem Harry Potter's Veela heritage adds a new dimension to her character. It often brings in unique magical abilities and a different social dynamic at Hogwarts. Another could be 'The Veela's Path', where the fem Harry Potter struggles with her Veela nature while also dealing with the regular Hogwarts challenges like exams and friendships.
One great 'Harry Potter fem phoenix' fanfiction could be 'The Phoenix's Daughter'. In it, the female phoenix character has unique magical abilities and plays a crucial role in the wizarding world. It's a story filled with adventure and mystery.