I usually try to name my ships after the class name
USS Zulfiquar, Excalibur-class -- Named after the sword of Muhammed. Fitting for a class apparently named after swords.
USS Andromeda, Galaxy-class -- Because I'm convinced Gene Roddenberry's "Andromeda" was meant to depict the Fall of the Federation.
USS Kadesha, Oracle-class -- A kadesha was a sacred priestess from Mesopotamia. It fits in with the Oracle class name.
USS Hecatoncheries, Fleet Escort -- She's a torpedo boat. Throws lots of torps at things, hence the name 'Hundred-Handed Giant.'