Jakob Nielsen wrote a 1996 column that criticized frames. Some key points:
Frames prevent users from properly bookmarking pages. When a bookmarked frameset page is loaded, users' previous mouse clicks inside the frames do not matter. Only the outer URL is saved, and users have to navigate to where they were manually.
Frames present challenges for printing web pages. Printing all the frames at once is not suited to the different dimensions of paper (and users can get only the first pageful that way). Users generally have to right-click the frame they want and choose the appropriate context menu option.
Users coming from search engines may not have access to navigational elements if they are located in another frame — they are directed to only that frame the search engine found the text in.
While "framesets" (the most common type used on late 1990s/early 2000s web pages) are dying, the iframe (short for inline frame) remains alive and well. In fact, recently iframes have been found useful in today's "mashup" web applications, and extensions to the iframe are currently proposed in the HTML5 specification.
For example, Facebook, in its API for app developers, uses them to seamlessly integrate third-party apps with their own site while minimizing the security risk. (In this model, all third-party code remains on a separate domain, which is good for security reasons.)
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