For some code as follows, 

    opts, args = getopt.getopt(sys.argv[1:], "c:", ...
    for o,v in opts:
...
        elif o in ("-c", "--%s" % checkString):
            kCheckOnly = True
            clientTemp = v

If I don't give the parameter after the -c, I get the error messages as follows.

Traceback (most recent call last):
  File "niFpgaTimingViolationMain.py", line 100, in 
    opts, args = getopt.getopt(sys.argv[1:], "hdc:t:",[helpString, debugString, checkString, twxString])
  File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/getopt.py", line 91, in getopt
    opts, args = do_shorts(opts, args[0][1:], shortopts, args[1:])
  File "/System/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/getopt.py", line 195, in do_shorts
    opt)
getopt.GetoptError: option -c requires argument

Is there any way to catch this error, and process it to print something like this? It seems that just wrapping the code in try/except doesn't work.

ERROR: You forgot to give the file name after -c option
the correct answer is to use the OptionParser module instead of trying to "roll your own".
How to process python generated error messages my own way?