Bear in mind that voxels are just a concept. There are several ways of handling them as data, and several ways of visualizing them (extract geometry, raycasting, ...).
It's a data point in a fixed-spaced grid, that's it. What this point represents or which geometric primitive you associate with it, that's totally implementation-specific. People usually visualize them as cubes occupying the entire cell in the fixed space grid, that's why you associate them with cubes.
The most famous/popular voxel-based application, Minecraft, visualizes them using the standard rasterization pipeline as cubes centered on a grid. (Academic) Systems like GigaVoxels perform ray-tracing into a Sparse Voxel Octree structure to generate images.
I've encountered the following voxel-oriented libraries:
- Field3D: Sony Pictures library for storing voxel data: http://opensource.imageworks.com/?p=field3d
- OpenVDB: A new format released by Dreamworks Studios: http://www.openvdb.org/index.html
- Polyvox: Used for several games, in active development: http://www.volumesoffun.com/polyvox-download/
- VoxelIQ: Game-oriented block-based engine in C# - https://github.com/raistlinthewiz/voxeliq
- GigaVoxels: Ray-guided streaming library for voxels - http://gigavoxels.imag.fr/
- Binvox: Not really a library, but a voxelizer with a basic binary voxel data definition: http://www.cs.princeton.edu/~min/binvox/
- VoxelFarm: An engine for generating procedural voxel terrain: http://www.voxelfarm.com/vfweb/engine.html
- cuda_voxelizer: A tool to convert polygon models to voxel models, outputs to various formats: https://github.com/Forceflow/cuda_voxelizer
And here's a reddit post with 20 years of voxel engine code: https://www.reddit.com/r/VoxelGameDev/comments/3fvjb4/20_years_of_voxel_engines_source_code_included/