I'd guess the ships have some sort of garden area (Where they grow fresh food and oxygen, of course, probably using bioengineered plants to produce more oxygen and such). Lights would probably be dimmed to simulate day and night, shifts would be rotated between the artifical times.
I suspect they'd have some sort of astronomy room, that could be used to simulate night outside with a projection/hologram of stars and well-placed speakers. (In battle situations, it could be used to plan ship movements and get an idea of the tactical/strategical situation.)
Some rooms like the 'main hall' might not be too unrealistic, since it would help with any sort of claustrophobia. I doubt they'd have a glass window though.
On anything lower than a Destroyer, they'd probably have the astrolab and hydroponics room, but lack any really large rooms. Possibly combine the two and use a smaller compartment as a tactical monitoring room.
Depending on how large, obtrusive, expensive, and effective the technology used for star projections then would be, some ships might add a star projection system to the hydroponics room with the outside simulation sounds.
