IPKat has a very nice analysis, as usual, here:

http://ipkitten.blogspot.com/2009/01/breaking-news-wto-panel-report-on-us.html.

However, IPKat concludes that it's more of a score-draw than a loss by the US.

Exactly. In many cases, patent offices only conduct prior art searches on previously filed and published applications. Getting exactly what it is you do into prior-art-space is a useful defence against another person later alleging patent infringement on a subsequently-filed patent.

Interference in national policy by other countries has been historical reality since time immemorial. It's been called under the name of treaties, representations, concords and, ultimately, declarations of war. EU, for all its faults, is still an excellent method of persuading countries which historically have been over-eager to take up arms against their neighbours to dissipate their tensions in very long, very dull negotiations over the European Standard Paperclip. I'd rather have that than the regular European wars of the preceding centuries. The EU may be expensive and inconvenient to some degree; the alternative is far more so.