For "a collection of maps":
* Map collection
* Cartographic compendium
* Gazetteer
* Road atlas (if specifically for roads)
* World map (if it covers the entire globe)
For "the first vertebra of the spine":
* First cervical vertebra
* C1 vertebra
* Vertebra prominens (though this refers to the most prominent vertebra in the neck, which might not always be the atlas)
For "a mythological figure who holds up the heavens":
* Titan (in general)
* Bearer of the heavens
* Sky-bearer
* Atlas, the Titan" (the specific name)
Remember that the best synonym will depend on the specific context of your usage.