PBS or TBS, where cannot use each buffers?
I think you answered your own question. 

The buffer used in a given experiment depends on the requirements and limitations of the experiment itself. You just have to look at the properties of the buffer, and if it is relevant to your experiment. 

You just gave two great examples... are you just looking for more examples of experiments when one would not use phosphate buffer vs Tris buffer?

PBS is supposed to closely mimic/represent the osmolarity of a cell, and buffer from pH = 7.0 to 9.0. Tris also buffers around neutral pH. It is pretty cheap, but as you've stated, has primary amine groups that are nucleophilic and thus interfere with certain experiments like disuccinimidyl suberate crosslinking, etc.