Microsoft Visio and Adobe InDesign and Illustrator are popular source programs for producing layered PDF files. Visio gives you the power to use one document structure and layer the information and data as needed. InDesign and Illustrator offer collections of PDF presets for export, and you can specify separate layers in most of those presets.
Why Bother with Layers?
In some cases, you should always flatten a document, such as a drawing certified by an engineer, to preserve its integrity. In other cases, feel free to layer away. A layered PDF document can be a terrific advertising tool. Instead of showing your customer one product image and some color swatches, put the alternate colors on different layers and let your client click through bookmarked layers, viewing the product in its varying colors.