While you could probably top a pretzel with almost anything, there are certain toppings and combinations that work best.
Coarse salt is always a favorite. You can find "pretzel salt" at many cooking and baking supply stores, as well as select gourmet markets. Substitute another coarse salt if you can't locate it, but stay away from fine table salt — the fine grain can melt into the pretzel as it bakes, and you won't get the same wonderful "crunch" you get with coarse salt.
You can also try one or a combination of seeds, such as sunflower, pumpkin, poppy and sesame. Some herbs and spices also work well as toppings.
Top the pretzels with the salt and/or seeds right after they come out of the wash so the toppings stick, before the wash has a chance to dry.
Other toppings are best added shortly before the pretzels are done baking or after they are removed from the oven, to keep them from burning in the oven's high heat. Top pretzels with grated cheese (or a blend of cheese and herbs or spices) a minute or two before they come out of the oven so the cheese has a chance to melt without scorching.
Freshly baked pretzels can be brushed or dunked in melted butter before topping (the butter will help the toppings to stick). Sprinkle over cinnamon sugar, or a blend of spices and grated dry cheese (such as Parmigiano-Reggiano).
Consider drizzling over melted chocolate, or just go all out and dunk the pretzels in chocolate before serving.
— Noelle Carter