I'm cross-posting this (also on Mathematics stack exchange, but not really getting the answers I'm looking for, so thinking I may have posted in the wrong community originally).
I've hit a roadblock with pgfplots where it has difficulty plotting multiple functions at the same time in 3D. As it states in the manual on page 114, "it cannot combine different \addplot commands, those will be drawn in the order of appearance." So something that should be behind another object might not be if you plot it last.
Does this same roadblock occur in gnuplot and Asymptote? I'd prefer to stay open source, but will move to Mathematica or Maple if I have to. And the quality/prettiness of the graphics is important to me, which is one reason I wanted pgfplots to work!
Edit: to clarify, I want something that looks professional and nice enough to inclue in published books.
I'd like to be able to plot general 2D and 3D functions. I need to be able to type in the mathematical function (rather than generating and inputing a table of data). In some cases, I may need to plot many functions on one plot (as mentioned above, this caused problems with pgfplots). I'm honestly not sure what specific examples to give, but if there are any shortcomings with gnuplot or Asymptote (or other programs) with 2D or 3D plotting, that would be nice to know!