Recommended (free) software to plot points in 3d I am looking for (preferably free) software to:
1) plot 3d points read from a file. A scatter plot would be fine.
2) Optionally color the points by a property - also read from the file  
It would be terrific if this program could also compute and display the best fit plane through these points.
 A: I checked all of the above options out and if you want to plot something in 3D in the next ten minutes, and not ten days from now, check out Graphing Calculator 3D.
A: Asymptote vector graphics language. Check out the gallery of graphs/plots/sketches. Here is very pretty examples/code page from France.


A: Another one is Plotly, which is entirely web-based and free for public use.

Disclaimer: I help develop Plotly
A: DataMelt math program for numeric and statistics computations looks good for plotting functions, data and histograms in 3D, and saving outputs in vector-graphics formats.  It is free and written in Java (so, runs on any computer). It is also portable, so no problem with installation.
Here is one example of function and a histogram: 
A: There are quite a number of freewares which do that.


*

*Gnuplot, with a very interesting not so frequently asked questions here (archive version), fit is easily obtained. Nice outputs to PDF and LaTeX

*Matplotlib: requires Python, so that's probably not your best option if you need to produce graphs quickly, but if you are thinking about a long term solution, I would go for this one,

*R, normally for statistical computations, but quite nice plotting possibilities. Also, it is a software which is intended to read data in files, so it has very powerful and easy to use functions to import CSV files and the likes,

*Octave not a big fan. Don't know the new major release, though. Previous releases were based on Gnuplot for the graphic part,

*Scilab has continuously grown througout the years, so as to become a monster now. Not a big fan either.


Hope you'll find your best choice here !!!
Good luck,
Sébastien
A: There is also MayaVi2:
http://mayavi.sourceforge.net/
But I am not sure how it compares with other visualization libraries...  would like to hear more comments on it.
A: I personally prefer to use GeoGebra, it has simple plotting functions and nice 3D graphing as well. To input a point, all you need is the ordered triple and it will plot it for you. It can also graph spheres and the like.
Hope this helps.
A: Look at maxima draw vtk .
One criteria that I apply to 3d graphs , is that they
have proper perspective. By this I mean that lines and
objects appear smaller the further away from the viewer
they are.
Also hidden line and surface.
 Three dimensional rotation ; scaling.
Real time updating.
Finally , maybe ray tracing.
A: I'm coming late on this thread, but geogebra: https://www.geogebra.org/ is a great simple tool. 
It can run in a web browser and it's very easy to use. 
