Fool's War by Sarah Zettel has an emergent AI in a mechanical ship. If you stretch the point, The Two Faces of Tomorrow by James P. Hogan has one in a mechanical space station. The Helix and the Sword by John C. McLoughlin has biological space ships and stations (not sapient, IIRC), though not as major characters. The latter volumes in Thomas A. Easton's "Organic Future" series have biological starships.
Bill Starr has a "damaged human bonded to starship" character in The Way to Dawnworld and The Treasure of Wonderwhat. They're far from significant plot points, but there are living sea-faring ships in The Crucible of Time by John Brunner and Harry Harrison's "Eden" trilogy. (Crucible wins points for being one of the rare novels without humans/humanoids.) There's a sapient biological sky-city in The Quiet Invasion by Sarah Zettel.
Moya on the Farscape TV series was sapient. While not a major player in the two Farscape novels I've read, there are several other novels and anthologies. The AI leading the generation ship in Kevin O'Donnell Jr.'s Mayflies is sapient and a significant character. John Varley's Titan series has sapient biological space stations.
Last edited by Jadon; 04-09-2011 at 09:26 PM.
Reason: more examples