Thanks for the reply

I have looked at those chips right at the beginning, but they're around $22 each in single qty's, not including shipping from LT themselves!. Element14 don't seem to stock the newer models.
The uC I was going to use is the ATMeg32u4 with 12 ADC's.
The main reason I want to do it with the uC is so that I can print the cell voltages on a LCD display. I can get a complete, 200W charger and balancer with a LCD from hobbyking for around $40, I'm tempted to open it up and have a look at how they monitor individual cell voltages onto the uC.
Hmm, looking at this charger I have here, and also basically ALL the multi-cell chips, they ALL seem to use a MUX. Is the purpose of this to allow the chips AREF to be changed to the next lowest cells voltage, so that your readings of the current cell are based on a "gnd" reference of the cell below?
EDIT: Thanks to Dave creepishly doing a teardown on a very similar charger to the one I literally just opened up, and providing a schematic, it appears I have my solution:


Just one thing though, will this still work properly if the ATMega is being powered from the battery it's reading? I don't think the grounds would be isolated in the charger, but I'm not sure.
EDIT: Looking at the schematic, I really don't see the point of putting the battery - through a divider then into the mux? What's the purpose of that? Possibly to isolate the batt - from the uC? Can anyone explain?
Cheers,
Dan