GCC 4.8 is currently out-performing LLVM/Clang 3.2 for the HMMer workload on the quad-core Core i7-3517UE Ivy Bridge processor with Hyper Threading.
MAFFT also had a slight favor to the latest GCC code over LLVM/Clang.
The MrBayes performance continued the trend of GCC 4.8.0 running ahead of LLVM/Clang 3.2 on the Intel Ivy Bridge hardware.
John The Ripper heavily benefits from GCC since there's proper OpenMP support there for multi-threading but OpenMP remains unavailable for LLVM/Clang. There's work on bringing OpenMP support to LLVM, but nothing merged yet.