Large voltage spikes on charge pump output
I'm prototyping a small charge pump out of a NE555 timer. However, I'm getting some spikes on the output along the rising and falling edges of the timer.
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  What could be the root cause of this issue? The spikes seem to be pretty significant being about 100mV.


It would help to see the full schematic related to the 555 and the physical layout (i.e. a photo).

However some versions of the standard (bipolar) 555 are known for briefly crowbarring the power supply, on each state change of the output - this fits with the timing of the spikes you are describing.

The old Philips Semiconductors Application Note AN170 from 1988 called "NE555 and NE556 applications" says:


  Due to the nature of the output structure, a high power totem-pole design, the output of the timer can exhibit large current spikes on the supply line. Bypassing is necessary to eliminate this phenomenon. A capacitor across the \$V_{CC}\$ and ground, directly across the device, is necessary and ideal. The size of a capacitor will depend on the specific application. Values of capacitance from 0.01&mu;F to 10&mu;F are not uncommon, but note that the bypass capacitor would be as close to the device as physically possible.


In the 1980s, I remember sometimes using a pair of decoupling capacitors (one small, one larger) physically next to the 555, to reduce the power-supply spikes to manageable levels.

Therefore I recommend you investigate whether such power-supply spikes are the cause of your issue, since the fact that they occur when the 555 output changes state on your 'scope pictures, suggest they could be related to this issue.


  Are the large spikes caused by the fact that this whole thing is being set up on a breadboard at the moment? If I shortened the leads and built this on a prototyping board, would it help?


Impossible for me to say for sure, until you have done more troubleshooting. However, if there is a lack of decoupling and/or you have long power-supply leads, then those won't be helping.