I've been thinking about this, and I've come to the conclusion that the One Piece story arcs deserve better names than "Arlong" and "Enies Lobby."
Here are some suggestions:
Romance Dawn: this one is fine, really. It sums everything up.
Morgan arc: probably "Pirate Hunter Zoro" or "The Pirate Hunter."
Buggy arc: "Buggy the Clown." He's evidently an important character, and I can't think of any other central theme, except maybe "Real Treasure."
Kuro arc: "An Honourable Liar." It's all about Usopp, right?
Krieg arc: "The Strongest Man in East Blue." Referencing Don Krieg, Luffy, and Hawkeye.
Arlong arc: "Tears of a Witch," referencing Nami's reputation on the island and the painful retribution for making her cry. Another possibility would be "Superior Being," but maybe that should be saved for the upcoming Fishman arc(?).
Logue/Roguetown arc: "The Legend Begins." Heck, it's even a chapter title!
Laboon arc: Simply "Laboon" or maybe "Promises." A short title for the shortest arc, right?
Whiskey Peak arc: "Welcome to the Grand Line" sums it up nicely.
Little Garden arc: "Instinct" might be a little too unspecific. "A Matter of Pride" fits a little better, although any suggestions would be welcome. Something with giants in the title?
Drum arc: "The Doctor's Dream." Referencing Hiliruk and Chopper.
Alabasta arc: "Shadow Over Alabasta." 'Nuff said.
Jaya arc: "Reach For the Sky." Or something mentioning dreams.
Skypiea arc: "The Light of Shandia." "Wrath of God" gives away too much.
Longring Longland arc: What could fit better than "Davy Back Fight"?
Water 7 arc: "Web of Deception," "City of Water," all those are good.
Ennis Lobby arc: "Demons of Ohara." Referencing Government persecution as well as Robin's own personal demons.
Water 7 arc II: "Ship of Dreams."
Thriller Bark arc: "Land of the Dead." Spoken by Moria. Seems to be the truth.