Which programs could be used to check the integrity of PDB files? And by that I mean recognize the (minimum) standard PDB format, check if there are missing residues (according to numbering in ATOM lines), missing atoms (according to residue identity and apart from hydrogens), non standard amino acids. I am pretty flexible for this task regarding programming languages, algorithms, personalization of runs, etc. I only need the programs to run in a Linux command line, provide an easy to parse output and be freely available for academic modification. However it would be interesting to make a point-by-point comparison if a big number of programs are available.
Most "servers" will check for physicochemical parameters as they expect a PDB file in good "shape".
I would use something like a traditional PDB Parser, like Biopython has for instance. It will complain about the wrong format and chain breaks (missing residues, for missing atoms you need a topology.. but you can easily build that) just by attempting to parse a structure. You can then check if you have non standard residues, and other personal checks by scripting them manually but it should be pretty straightforward if you have some knowledge of programming.
Finally, for some "correction" tasks you can use one of these servers: http://swift.cmbi.ru.nl/servers/html/index.html