If the panel is not mounted on the car yet, an "ironworker" (various makes/models) is the way to go, one example attached. I've got one at work, with a plethora of die shapes and sizes. You certainly won't be spending $10K for a couple holes, but you might know someone with access to a tool like this.
If it is in place on the car, as Bob mentioned there are two piece punches (with mandrel) that come in various shapes and sizes. You drill a hole first for the mandrel (which is smaller than the die), and then torque down on the die, either with a ratchet (poor mans version) or with a hydraulic ram. Electrical based tools are the most popular. Google "Greenlee Hole Punch". A sample picture is also attached. The most common as you can imagine are for 1/2, 3/4, etc. conduit fittings, and they are round. But there are many many sizes and shapes out there, you just need to look.
With a mandrel based tool, you really need to get the exact shape die. With an ironworker, you can if needed use smaller dies and nibble away at making a larger shaped hole, making it much more versatile.
