Apple has already told us that they will support open epub files. Ultimately, the best option is you can just drag and drop your epub just like music files into your iTunes and sync them. This would likely be for iBooks access only.
It's no shock that Amazon is squashing Stanza when Amazon wants to push their ebook reader/delivery system for the iPad. The good news is there are dozens of other book readers and another one that wasn't bought out by Amazon will come to the forefront. Personally, I really like Txtr better than Stanza. All the epubs I've looked at (my own creations), format better in Txtr.
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