There is fairly new VW Eos Tech Service Bulletin 61-07-11, released December 17, 2007 that provides a dealer techs with an extensive procedure for inspecting the top seals, and for repairing the existing top seals if the inspection finds that they were not factory applied correctly or have factory defects. This TSB provides very large # of time units for both diagnosis and repair actions and directs that it be charged back to VW as a warranty repair.
It does not allow replacing entire seals or the entire top - there is a repair action that is not that drastic for all leak locations discussed in the TSB.
This TSB seems to recognize that there are many more than one root cause for water leaks on 2006 and 2007 manufactured VW Eos.
Some things being inspected for in the TSB is some seals were inproperly installed, seal areas got glued down that should not have been, so the sealing surface is not where it needs to be, it is too low or at the wrong angle. The TSB provides procedure to add butyl cord to get the seals lifted to the right angle to get the sealing surface where it should be if need be.
Lots of other actions in the TSB besides that one, too.
Next time I drive my Eos in a good soaking rain I am going to go over the car carefully to make sure it is not getting water in the passenger compartment on either side or the trunk or in the spare tire well. I suggest we all do the same.