The Force-Atlas2 algorithm [1] has some benefits over the force layout implemented in d3.js, when you want to highlight the communities structure in the graph. A javascript implementation is found in the library sigma.js [2].

Other basic layouts are the circular and random ones [3].

Gephi [4] has a variety of graph algorithms, about 10.

[1] http://journals.plos.org/plosone/article?id=10.1371/journal....

[2] http://sigmajs.org/

[3] http://www.lexmath.com/grafos/sigma/ejemplos/a_plugin_exampl...

[4] http://gephi.org/

Edit: added gephi to the list.

Recommendations from my coworker (https://twitter.com/Amust1987):

Try to read this paper. They mentioned several graph layout algorithms.I think you can also try to ask them the source code. http://www.cs.ubc.ca/labs/imager/tr/2006/Archambault_TopoLay...

Also this paper might be interesting as well. It concludes and categories graph layouts algorithms. Depending what information you want to visualize and what the data looks like, you can pick up different algorithms. http://profs.etsmtl.ca/mmcguffin/research/2012-mcguffin-simp...

Recent discussion of a drop-in force layout module based on a more general constraint-based algorithm (WebCola)

https://news.ycombinator.com/item?id=9840875