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How does this work? please explain. I'm not getting it.

would 1N4148 do?

Also, the regular non-zener diodes, I had thought that if they conduct in reverse direction then they are broken forever.

Right, you want one diode with its anode connected to Gnd, its cathode to the transistor's collector. Then a second diode connected the same way, anode to collector, cathode to +5V. 1N4148 will be fine.
What happens is, if a spurious pulse drives the collector more than ~0.6v below Gnd, the diode conducts and clamps the spike to Gnd.
The same with the upper diode, except this time any positive going spike gets clamped to +5V!

 

Exactly. It is a standard way of clamping voltages to just beyond the supply rails. Nearly every input in a microcontroller has this protection. Without that, they would fail all the time.

 

Here's the schematic. All is working fine except the photo transistor keeps going bad.
View attachment 304318

If this is the real schematic, it can't work properly.
It needs bias voltages for the opamps.

 

If this is the real schematic, it can't work properly.
It needs bias voltages for the opamps.

Can you elaborate on that? What is bias voltages? Why is it needed?