warning: skipping file '/Users/jounimiettunen/svn_iphone/project/trunk/protobuf/ProtocolBuffers.xcodeproj' (unexpected file type 'wrapper.pb-project' in Frameworks & Libraries build phase)
It means that building or linking something failed, in this case ProtocolBuffers static library. Possible reasons are missing "Linked Libraries" and/or "Direct Dependencies" definitions or that building those failed.
Possible Fix: make sure your target (Info - General) has correct setup. If you're using Apple SDK 4.0 add -ObjC into "Other Linker Flags" and also -all_load to force loading of everything. Make sure you do this for both project and target. More info at Mac OS X Reference Library "Technical Q&A QA1490": Building Objective-C static libraries with categories.