When starting with HMMer, GCC (both 4.7 and 4.8) are much faster than LLVM or even when using GCC with DragonEgg. It seems LLVM's optimizers are not as good as GCC's for this scientific benchmark. When DragonEgg was used while also enabling the GCC optimizers, the performance returned to nearly matching that of the vanilla GCC.
MrBayes was also the fastest with vanilla GCC over LLVM in any configuration -- Clang or DragonEgg. When attempting to use the GCC and LLVM optimizers with the extra compiler switch, the build failed.
LLVM finally comes out ahead when it comes to the KASUMI test within the Botan crypto library. LLVM with the Clang compiler front-end did the best while GCC with DragonEgg also was close with its performance and well ahead of a plain GNU Compiler Collection setup.
The other Botan crypto tests were mixed for who has the best compiler on the Intel Core i7 Linux setup.