RC guys do it -- they've even added it to the nomenclature: a "4S2P" pack has two packs of four series cells each in parallel.  I haven't done it myself, but my understanding is that as long as you use batteries with like number of cells and like chemistries you should be OK.  If you use two "identical" batteries purchased from the same place at the same time you should be as right as rain.

I'm a little surprised that you feel you need to do this -- is it to get the pack to fit?

Hi Andy,
Ideally, you want to charge/balance both packs and then merge the balance connectors so the paralleled cells discharge as a single group.
You got a funny shaped battery compartment?
Dean

There seems to be a feeling (by some fairly smart folks) that longer battery wires are implicated in ESC failures.  From an electrical design standpoint I can't see this -- the last brushless motor controller that I helped design operated just fine on a 100 foot extension cord from its main 28 volt supply -- but it comes from people that are hard to ignore.

So if your motors are in nacelles, then having one battery per motor, mounted in the nacelles, would be a nice way to go. 

Even if the "long battery wires kills ESC" thing is an urban legend*, wires with lots of current flowing through them burn up power, and the longer they are the more power they burn up.  You can reduce the amount of power burnt by going to thicker wire, but -- that's "thick" as in "heavy". 

So short battery wires is good battery wires.

* There are some good solid reasons why long motor wires would kill ESCs, by the way.