Amy normally paints her nails in her room. She has since the day she started traveling with the Doctor. She paints them all kinds of colors: reds and blues, greens and oranges, the color blarg from Belforem Six (which is somehow blue and yellow at the same time). Sometimes she'll use her polish in other rooms, but only when the Doctor and Rory are there and she moves her production to spend time with her boys.
Amy is very careful about her nail polish. If the bottle tips over or a drop falls from the brush she immediately cleans it up. She keeps track of every bottle so that she doesn't end up losing her favorite shade on some alien planet.
Amy likes her nails to be perfect. She refuses to touch anything while they're drying, and she makes the Doctor or Rory do anything that can't be put off. She never paints her nails in the control room; it's always shaking somewhat and the movement make it difficult to avoid painting her cuticles.
So, Rory reasons, there shouldn't be smudges of pink on the captain's seat. And there shouldn't be a half-used bottle of 'Morning Rose' color jammed in a small crevice in the bottom floor of the control room. So Rory fishes the bottle out and sticks it in his pocket to give to the very busy Doctor later. He thinks that the Doctor may want to put the bottle of nail polish in his "room of old companions' things", if such a room exists.
Rory doesn't remember the polish until he's headed off to bed. "Doctor," he says, turning around, "I found this earlier." Rory pulls the small bottle out of his pocket and offers it to the Doctor. "I's not Amy's. Thought you might want to put it somewhere."
The Doctor takes the bottle slowly, a look of sorrow coming over his features. "But she was never in this room," he whispers, "The desktop changed after I regenerated."
"There're also smudges of it on the seat," Rory says even though he's pretty sure the Doctor's not hearing him, "I could clean it off…"
"No!" The Doctor's head snaps toward Rory, fierce passion in his eyes. "Just, just leave it."
Rory senses that he shouldn't say anything else, so he just turns and leaves. He's barely out of the room when he thinks he hears the TARDIS hum sadly. He looks back to see the Doctor slowly stroking part of her controls. "I know, old girl," the Doctor whispers, "I miss her, too." Rory makes himself walk the rest of the way to his and Amy's room before he allows himself to wonder about the identity of 'her'.
Rose Tyler was never careful with her nail polish.