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The landscape has become simpler in the past few months. It is now essentially everyone against Amazon.
Amazon uses two formats AZW and TOPAZ. AZW is a variant of MOBI, and its DRM (encryption) can be circumvented, so if you are willing to strip DRM AZW ebooks are "future proof". TOPAZ ebooks are Kindle-only, and are usually not available in any other format. The vast majority of Kindle ebooks are AZW, but some categories are more TOPAZ heavy than others.
Everyone else uses Adobe ePub. There are a few migration issues (Sony from LRX to ePub, and B&N from eReader and adding a 2nd DRM scheme to Adobe ePub), but there are already a wide range of EInk devices that read Adobe ePubs and it seems that in the medium term (e.g. by this time next year) they will all inter-operate. In the long term no encrypted ebook format is guaranteed to survive, but the good news is that Adobe ePub DRM has also been circumvented. DRM-free ebooks can last forever, because format shifting software (like Calibre) can keep the ebook working on all new devices.
Kindle is dominant enough that it is still a reasonable choice for the long term, but ePub is the best bet going forward. This does not restrict your choices much today.
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