In-N-Out's "Secret Menu" allows for a lot more variety, but, yes, not as much as other burger joints.

Here are some examples from the Secret Menu:

2x4: Two meat patties and four slices of cheese. (Note: You can get any combination you want, even as enormous as 20x20. Order is layers of meat, then layers of cheese.)
3 by Meat: Three meat patties without cheese.
Animal Style: The meat is fried with mustard served on a bun with pickles, lettuce, tomatoes, extra spread and grilled onions.
Animal Style Fries: Fries with cheese, spread, grilled onions, and optional pickles.
Double Meat: Double Double without cheese.
Flying Dutchman: Two meat patties, two slices of melted cheese and that's it. No bun, no lettuce, nothing.
Fries "Light": Almost raw fries.
Fries "Well-Done": Extra crispy fries.
Grilled Cheese: No meat, just two slices of melted cheese, tomato, lettuce and spread on a bun.
Neapolitan Shake: All three shake flavors (strawberry, vanilla and chocolate) combined in one shake.
Choco-Vanilla Swirl Shake: A chocolate and vanilla shake in which the two flavors are swirled into one another.
Protein Style: Instead of a bun, the burger is wrapped in lettuce (Atkins approved). And yes, you can get a Grilled Cheese Protein Style!
Veggie Burger: A burger without the meat and cheese.

Just a few of the options that aren't up on the basic menu.