Heinlein had several:
- Methuselah's Children (memory fuzzy but pretty sure as Dora is part of the Lazarus Long/Howard Family short stories as well as the novels)
- Time Enough for Love
- The Number of the Beast (perhpas far from his best work but readable)
- add to this many short stories about the Howard Family and Lazarus Long where these ships come in and out of the plots.
Also with not a ship but a sentient computer system was The Moon is a Harsh Mistress
The Hal Spacejock books
by Simon Haynes who is a member here, there are four, also have an AI ship, and sentient robots as well.
I think there might be a couple more but I don't recall at the moment.