Most use spaceships (although the difference is really just cosmetic), but I can't be bothered to list them all (there's around 60-70). There are also various TinyMUDs which utilise ships, but they tend to handle it somewhat differently, so I've not bothered with those either. I've also skipped some of the more tacky implementations, and I've no doubt missed many muds which didn't use obvious keywords, but here's a few to get you started:
Necromium: necromium.com 4000
5 Kingdoms of Mercator: xerxes.mudhaven.com 2411
Merentha: merentha.com 10000
Duris: durismud.org 6666
Elysium: elysium-rpg.com 7777
Basternae II: 131.128.194.236 6666
Dark and Shattered Lands: dsl-mud.org 4000
Abandoned Reality: abandoned.org 4444
Empire: wraith.aplus.net 4000
DarkWind: darkwind.org 3000
Ancient Empires: mud.ancientempires.net 5011
Xyllomer: xyllomer.de 3000
Beyond the Forest's Edge: tfe.genesismuds.com 2000
Waterdeep: wdmud.com 6660
Nemesis: mud.nemesis.de 2000
ElderainMUD: elderainmud.com 4000
DreamsMAZE: sonad.com 4208
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