Near the end of the final season, Miyuki has just walked away from the scene of an accident to find help after she and another car fall off of a cliff, and passes out from exposure to the rain, her own injuries, and exhaustion. She then has a dream where she meets Ken on the roof of their precinct building and he proposes to her. She wakes up to find Ken who, despite having a broken arm, is carrying her to safety on his back and begins saying the exact same words as Miyuki heard in her dream. She says yes.
Even earlier, during Sena and Daimaru's wedding, there's the scene where Ken is supposed to get a kiss on the cheek from Sena after winning an impromptu race. He actually gets one from a Miyuki who, upon Sena's request, has put on the wedding gown and poses as the bride.
From File 48: The End of Summer
Natsumi clocks out early so she can get to the airport in time to give Toukairin a piece of her mind, for throwing their last arm-wrestling match, and for leaving without telling her how he feels about her. She barely lets him get a word in edgewise, 'til he stuns her with a "Shut Up" Kiss. Natsumi recovers a few moments later, then says it herself.
One early episode in Season 2 has Miyuki spend all night with Nakajima simply teaching him how to send an email as he was entirely new to using a computer. At the end, he sends her a simple "Thank you" message, and the final shot is her making sure to save it to a folder where it will never be deleted.
Any time Nakajima's actions prove his feelings for Miyuki, most notably taking a shot for her, twice.
In season 3 when they find a little girl who mistakes the Chief for her recently deceased father, Natsumi arranges for her and the Chief to take the little girl out for a trip so that she can be with her "Papa" one last time.
When she finally realizes that the Chief isn't her father, she then develops a Precocious Crush on him after seeing how cool he was when he jumped onto a moving truck to save the driver who had lost consciousness. Also counts as a Crowning Moment of Awesome for the Chief.
During the final episode of the final season, after hearing a joke from Natsumi about them quitting the force and getting married, the three kids (Yuta, Sho and Maho) all come to the station to plead with them not to do so.