Undervoltage from solar panels So i'be been toying with the idea in my head of creating a solar powered weather station with an arduino, two 6V 2W solar panels in parallel, two 5V USB battery packs, and an adafruit module which converts voltages from 3-12V to 5V (to charge my batteries). I'm also working on using some small relays or MOSFETs for the arduino switch between batteries. 

The problem: If my solar panel voltage drops below 3V, the adafruit board will supply the batteries with a n unstable voltage below 4.8V. I need some sort of circuit or sensor that is capable of detecting when the voltage  from the solar panels drops below 3.3V and which will open the circuit to protect the batteries from unstable voltages.
You have selected a number of things that don't go well together. It is possible to use relays or mosfets to switch between batteries, and the Arduino could be used to measure a voltage. Or you can make a circuit with a few electronic components (e.g. a comparator). However, no one does it like that. It would be unreliable.

Every solar power charging module can handle darkness as well. Some modules will also create 5V.

This Adafruit module has no 5V output, it only contains the charging part: Adafruit:USB / DC / Solar Lithium Ion/Polymer charger - v2
It is out of stock at the moment, and you need solar cells, battery, a cable, and a DC-DC converter to make 5V.
When it is dark and the battery is empty, I assume the output drops and the Arduino stops working. Adafruit made a tutorial for it that shows the DC-DC converter and also Collin shows a DC-DC converter: Youtube, Collin's Lab: Solar

There are other modules like that. For example the Sparkfun Sunny Buddy.

Take care that the batteries don't get too hot.
It is possible to run some Arduino boards directly from a battery (3.1 to 4.2V). Then you would not need the DC-DC converter.
Buy solar cells that are the best in low light conditions. With enough sunlight, the power is no problem. It is the dark winter days that could be a problem.