I like this. A few suggestions:
Add functionality for 1D arrays (vectors), it would be nice to have one stop shopping, and runmeaning a vector is quite a common task.
Add a step parameter,for example: Let's say I want a 13-point running mean but I only want this every 2 points, so I'm halving the size of the array along that dimension.
Add more padding options.
John, I saw in your zip file how you are thinking of removing method 5. Let me make a counter suggestion: expand it. I can think many of reasons and applications where a neighborhood average would be useful. In terms of expansion: Well, you could allow for the size of the neighborhood, its orientation (forward, backward, center), and the function (sum, mean, var, mode, etc.) to be passed as additional arguments. Either way, this function is very useful and I use it often in place of standard Matlab functions.