My personal web projects always start with standard-conforming HTML with forms and links. They're fully interoperable contributions to the world-wide web and should be usable by every browser and robot written in the last sixteen years. I call that a feature, and I'm disappointed that so many devs set their sights lower.
IE has a nasty habit of sniffing content or examining URLs and disregarding the actual media type of a resource, but it hasn't come up much in practice, and otherwise I haven't seen any showstopping problems in talking HTTP and rendering semantic HTML. Its CSS and javascript are a mess, but those are optional, and I'd be embarrassed to release anything that would become completely unusable without them.