Drupal 7 is just around the corner, and it has such an architectural paradigm shift to make it quite difficult for those trying to upgrade. There are handful of modules which will be deprecated due to changes in architecture (namely fields-in-core).  Content Profile & Ubercart, while not being deprecated, are likely to lose out their new brands Profile2 and Drupal Commerce respectively.  The big dogs CCK, Views, & Panels will likely be delayed on their upgrade paths because of the complexity.  Because of all this, you need to figure out how you're going to be running your upgrade.  There are two possible methods I see, and another method on which I'd like to hear thoughts.

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