Charging a 3.7v lipoly battery at less then 4.2v?
I have an Arduino


If you want low power, this isn't the best choice, as it contains lots of circuitry that you might not use but it will still draw power. So if you want to supply it from a low power microial fuel cell, make sure you check how much current each part on the board uses.


  The issue is its going to be low amp (I havent measure it yet) and around 0.9v. 


Would be a good idea to measure it...


  Will charging it this low even do anything? Assuming the battery charge will be higher than the MFC.


Nope.

A LiIon battery is probably the best choice here due to high charging efficiency. Also it has no "memory effect" so it can be charged when power is available, and its voltage range is ideal for most microcontrollers.

However you need to boost the voltage from your 0.9V fuel cell to charge the battery.


  would anyone recommend using a supercap to relay the MFC charge instead?


a supercap won't boost your voltage

Check energy harvesting chips, for example from analog/LT. Here's one that looks interesting. 

Even if you don't use it, reading the datasheet and app notes should provide useful information about what you want to do.