Raymond Chen has some thought experiments useful for discovering various kinds of stupidity in software design:
Tim Berners-Lee's principles of Web design includes my favorite: Test of Independent Invention. This has a thought experiment containing the construction of the MMM (Multi-Media Mesh) with MRIs (Media Resource Identifiers) and MMTP (Muli-Media Transport Protocol).
The Internet design principles (RFC 1958) includes the Robustness Principle: be strict when sending and tolerant when receiving. A good one, but applied too liberally can lead to interop issues. For instance, consider web browsers. Imagine one browser becomes so popular that web devs create web pages and just test out their pages in this popular browser. They don't ensure their pages conform to standards and accidentally end up depending on the manner in which this popular browser tolerantly accepts non-standard input. This non-standard behavior ends up as de facto standard and future updates to the standard essentially has had decisions made for it.