There are many examples when visualisation is not done in a good manner, see e.g.

Http://www.datavis.ca/gallery/

Well, there are a number of visual cues for depth that can enhance the 3-D experience, but are not available in many of today’s equipments -- and this often translates into insufficient information for a viewer.

I use a few free online visualisation tools. The ones I use are mostly website analytics tools provided by my webhosting company and Google analytics. I find that the data represented by a single service is not sufficient. I find that only after looking at all three services that I am reasonably confident that i have a general understanding what is happening with my website traffic. To directly answer your question, when I find a data representation tool is insufficient, I use a 2nd and 3rd tool.

Some work have been done on visual perception of distance, Gladwell we'll talks about the "picture problem", and Wolfram discusses some limits to our visualization capabilities as humans. Personally l'll look for inspiration from Edward Tuft's efforts when an existing method fails me-perfect combination between numbers and art.

http://www.wolframscience.com/nksonline/section-10.7

http://www.newyorker.com/magazine/2004/12/13/the-picture-problem

http://www.ncbi.nlm.nih.gov/pubmed/9090148

http://www.edwardtufte.com/tufte/