Two options come to mind, one free and the other not.
The free option (for Windows only) would be
Irfanview. Its batch conversion option can be used to crop to specified coordinates, rotate, etc, and it can automatically name the resulting files based on a template. One pass through your files would give you the "odd" pages and a second, with a different set of cropping coordinates, would give you the "even" pages.
The commercial software that I'd recommend is Vuescan, from
Hamrick Software, is available for Windows, Mac OS-X, and Linux. Despite its name, it isn't just for use with scanners - it will treat files from disk as if they were from a scanner. Assuming that your files are of uniform size, you can set the area you want it to "scan" on one file and tell it to process the whole directory, naming the resulting files automatically. You could definitely do two runs through the files, one for odd pages and a second for even pages, but I think you might also be able to use the multi-crop option to get both pages in one pass through the files. The only catch here is that I don't think Vuescan supports PNG
so you might have to convert to TIFF or JPEG to process the files (Irfanview will easily batch-convert files).
I love my Vuescan Professional software; I use it to scan everything to either RAW TIFF or DNG (digital negative) format, then use Vuescan again at a later date to process the raw files to produce a multi-page PDF or whatever I need. It's a truly outstanding piece of software with exceptionally good licensing terms (you get the right to install it on up to three computers for a very reasonable fee).