Two dimensional array of objects in as3

Sure, but you have to declare each object separately and you have to call index number instead of variable name

Say I have an array of colors with a sub array of types of that color filled with objects describing RGB

var colors:Array = [];
var red:Array = [];
var darkRed:Object = { r : 256, g : 100, b : 100 }
red.push( darkRed ); //darkRed is now part of red
colors.push( red ); //red is now part of colors

To access darkRed, you would do this:

colors[0][0]; //that is darkRed

I believe this is what you are trying to accomplish :

var countdowns:Array = new Array;
countdowns[bodyID] = new Array;
countdowns[bodyID][powerupName] = { time: powerup.getTime(), onRemove: onRemove };

The second dimension of the countdowns Array is achieved by inserting an array into each element of the first dimension.

While this certainly can be done, but it's possible you're overcomplicating things. Perhaps a single-dimensional Array ob tailored Objects will suit better.

var ob:Object=new Object();
ob.bodyId=bodyId;
ob.powerup=powerup; // direct link to powerup might serve you better!
ob.onRemove=onRemove;
countdowns.push(ob);