Modeling is the tool that makes the assets rendering is the tool that makes them into pictures. Since you want simple shapes you just want the output pictures so you only need the rendering back end. Because most render engines have primitives for squares and spheres.
In any case there are too many tools to enumerate comfortably. Ill try to summarize the choices by category. Im focusing on free or at least affordable tools as you can comfortably spend $10,000 on your infrastructure easily:
Software rendering makes for very flexible pipelines. The quality of software rendering is easier to control and do than in hardware rendering. Features such as global illumination and image based lightning is commonly available. On the other hand software rendering is usually a tad bit slower, tough some commercial renderers are pinnacle of computation fast. On the bonus side most software renderers are capable of doing micro polygon renderng, which means a sphere really looks round irrespectively of resolution.
All software renderers come with a easy to use programmatic and textual interface. And they are really easy to set up all you need is the rendering engine and a text editor. Choose a software render if: you need to do stuff as pictures, for commercials or webpages.
Example 1: A simple RIB stream
Translate 0 0 0
Sphere 2 -2 2 360
Cheap choices in this category are:
3delight. (one 4 core machine license for free) Its fast, and if speed is a concern you could swap over to Pixars renderman with no changes in pipeline, because it supports RIB which is pretty easy to author and has several programming bindings. The sub pixel rendering engine is going to make beautiful raster images. And because its commercial you can get additional support easily if you ever over exceed simple needs.
RIB is also standard so the first has some real staying power when it comes to recreating the work later that NO other rendering file format has. Quite many front ends can generate RIB data. Delight also comes with plugs for Maya and 3DS max.
Image 1: Simple example that ships with 3Delight demonstrating sub surface scattering (render time: a few seconds). Image color corrected from linear space to sRGB.
YafaRay, open source pretty easy to mesh with. Because its free you can use amazon for bulk rendering. I would use either this or delight on a company project.
Povray, could be a possibility but its a bit old and slow. Both yafaray and 3delight provide most of all povrays features.
Hardware rendering comes in two flavors, those that are meant for interactive use and those that are meant for offline rendering, for real time rendering i suggest
- Unity, which is a game engine. dont let that fool you graphs are trivial stuff for game engines. Unity is capable of making executables that you can show nearly anywhere even in the browser.
Many other engines exist, this is the programmer land and some of the other answers reflect this category.
- python + pylab, has all you need to make interactive 3d that looks pretty good.
PS: you may need to specify your data and your computer usage level in mnore detail to get a better answer.