The choice depends on that what it is planned to examine as a trend. If experimental conditions are supposedly the same as Kenneth suggests, more effective analysis can be carried out using the parametric refinement. Please, refer to:
G. W. Stinton & J. S. O. Evans, Parametric Rietveld refinement, J. Appl. Cryst. (2007). 40, 87-95.
For sure TOPAS does this due to the macro-language, and GSAS-II is now able to perform similar tasks.
Of course, I have calculate the bond distances and angles, even I have plot the thermal evolution of the cell parameters.
I mean, after doing the strutural refinement with the single crystal data at diferent tempertaures I get the same structure (cif files), but at different temperatures. I don´t know how to overlap all the asymetric units and unit cells in the same picture to see visually which are the most important changes in the crystal structure.
Hope you'll get non- over-crowded picture... Have suggested here and do it again to try out excellent (free-of-charge) VESTA (Momma & Izumi) drawing/structure software, I have never tried before plotting more than 2 pictures at the time, but you likely may find it suitable to do with an extended set of structures.
Also CCDC Mercury does it but having unlocked licensed full-featured version, or Materials Visualizer (BIOVIA) knows how to superimpose structures as well.
I use COMPACK. http://scripts.iucr.org/cgi-bin/paper?wf5008
Compack, written by Motherwell and Chisholm, compares structures by overlaying clusters of molecules and calculates a similarity measure in the form of an RMSD of the atomic cooridnates.
Another program is KPLOT. http://scripts.iucr.org/cgi-bin/paper?S0021889805032450
Kplot, written by Hundt, directly solves for the affine mapping between unit cells.
It's also possible to compare structures by their radial distribution function, not sure what software to use for that though.... Or you can compare their simulated powder x-ray spectra.
Generally what you have understood under 'compare' for crystallographic unit cells? Have you isomorphic structures? Ot you hav emeasured one an dthe same compound at different temperatures? Then what you would like to compare - geometry parameters, errors? If you have the last case then you need statistical software for chemometrics, having ANOVA and regression analysis (Origin, MathLab, StatWin, for example).