Structural superposition

MatchMaker which is part of Chimera
O
lsqman
lsqkab
coot
Theseus is a program that simultaneously superimposes multiple macromolecular structures. Instead of using the conventional least-squares criteria, Theseus finds the optimal solution to the superposition problem using the method of maximum likelihood.
Escet good for finding subtle differences, or the common core
Using CCP4i: go to the coordinate utility - Superpose molecules - You can either compare things using secondary structure or by specifying residue spans. Underlying programs are PISA (also available at the BI msd server) and LSQKAB
CCP4: superpose foo_1st.pdb [-s CID1] foo_2nd.pdb [-s CID2] [ foo_out.pdb ] Only bear in mind that superpose relies on the presence of secondary structure, so that your selections should always include at least 3 SSEs.
MUSTANG - http://pxgrid.med.monash.edu.au:8080/mustangserver/
FATCAT - flexible alignment
or just choose one of the 84 or so entries in Wikipedia