For my tastes:
Overall rating, In-N-Out wins out. The fresh, sliced-in-the-kitchen fries are better. Their food just tastes fresher. Whataburger is far superior to the big national chains (McDonalds, Burger King, Jack in the Crack, etc.) and has home field advantage.
In-N-Out Pros: the freshest of any chain, friendly competent staff, very clean, best shakes, grilled onions, still family owned (I think), all locations always the same quality and service every time, so popular they don't even need to advertise (that alone says volumes).
In-N-Out Cons: limited menu, a bit skimpy on the meat portions, they insist on putting thousand island dressing on everything (I have to tell them "no spread, mustard instead"), a California groove to the place.
Whataburger Pros: big menu, lots of variety, jalepenos available, big portions of everything, Texas toast, top burger chain from Texas.
Whataburger Cons: seems greasier than most fast food burgers, frequently slow, fries can be soggy, noticeable variation between sites especially regarding competence of employees/getting the order right.
Both easily beat out the big national chains.
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