Newlaunches.com has published a list of Top 10 Apple products which flopped, which is hardly a first but is certainly great link bait.
All such lists are arguable, and this one has a couple of major flaws. For example, it misses the Apple III and the Cube (not to mention the original 1984 Mac, and the QuickTake camera line), but includes the Motorola ROKR phone. How does that make any sense at all?
Taligent is on the list, but not Kaleida Labs, which was another Apple-offshoot set up with IBM as part of the deal to use PowerPC processors.
Other products that could be on the list are the Apple eMate (a version of the Newton, with keyboard, for education) and HyperCard, which delivered hypertext well before the Web. But it depends on your definiton of "flop". Both products failed to live up to expectations, but they weren't obvious clunkers like the Apple Portable, which was miles behind what was already available in the PC market. Indeed, I liked both of them quite a lot.