About Hot Start Taq DNA Polymerases - (Aug/21/2012 )
There will be differences in the buffers and potentially in the sequence of the polymerase, which may have been optimised for certain conditions. There may well be differences in the purity of the polymerases too.
Depending on your application, you can certainly use other polymerases, so long as you continue to use the same polymerase for all your samples, so as to not introduce a potenitial bias in your results.
Like Bob said, each polymerase works the best in the buffer that accompanies it.
You might have to change the reaction conditions a bit, if you are going to use a different polymerase.