In a series pass voltage regulator, where should the fuse be placed?

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A lot of unknowns.

Put a short across the bridge rectifier input and see if the mains fuse blows within say 5 seconds or, more scientifically, monitor the primary current and see what it is with a short.

Your assuming the fuse will blow... you have to prove it ! Very small transformers can even be inherently short circuit proof... and we don't know what you have.

As to a secondary fuse. It depends on the result of the first test. If the primary one doesn't blow then you need one to protect the transformer (and that will have to be rated to stand the reservoir cap charging current and perhaps another at the input to the regulator. Fusing the output of the reg could cause problems if the fuse isn't incorporated in the feedback loop and even when it is, its not always the best of solutions.
 
The fuse won't save the transistor if the regulated o/p gets shorted - no chance. A 0R1 resistor (assuming your PSU is a couple of amps or so o/p) in the emitter with a couple of series diodes base to the non emitter end of the resistor, plus a fuse, may save it though.
 
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