What kind of pie is this?

If you do this often I would make a little pastry cut out of the fruit type of the pie and use some egg wash to stick it onto the pie - it looks good and eases identification.

Label them before you put them away.

Use pictures of the filling in pastry on the top crust.

X-Ray machine?

If you properly vent your pies, you should be able to determine the difference by the color you see through the vent for fruit pies with two crusts. You can make some very pretty pies with large vents that look quite attractive. Even pies with a crumble or crisp topping should show a bit of their fillings in parts.

As with everything you put in the refrigerator and freezer, label and date it.

If it's a two-crust pie, you should be able to flip it over, and cut a small hole in the center, take out a core sample, and examine the interior.

Flipping them over is also one of the best ways of cutting many pies, since it will cause less damage to the sides, and thus a more visually appealing slice.