I have code that, right now, uses "int array array" to store lots of
things, but in some cases I run out of indices in the outer array (the
inner arrays are always fine, but I hit the max array length limit on
the outside).

I would be happy to switch over to bigarrays, but my understanding is
that 2D bigarrays have to be square.  I cannot possible have square
arrays (it would take too much memory).  Is there an obvious way around
this that I'm missing?

-- 
 Hal Daume III --- me AT hal3 DOT name  |  http://hal3.name
 "Arrest this man, he talks in maths."  |  http://nlpers.blogspot.com