At this point, the major factor holding back write-once run-anywhere binaries is that they generally require developers to conform to a particular language.

In my experience developers are EXTREMELY loyal to their respective environments (language and OS) and resistant to change, which is likely why this thread has ruffled more than a few feathers.

Additionally, write-once executables require that developers abandon often very well developed languages that have libraries of code and mature development environments. This is one reason (but only one) perl thrives despite somewhat poor syntax. There is tons of perl code available for re-use and easily accessed.

But there is light on the horizon. NaCL (Google's Native Client, and implemented using LLVM, FWIW) introduces a secure binary format for x86 that doesn't imply a single host language, just that .nexe files are produced. This allows developers to maintain their existing languages, and write code that's guaranteed to run at native speed regardless of the OS -- providing the appropriate compiler and NaCL clients exists.

With the introduction of PNaCL, these binaries can run across x86 and ARM, though as security is a paramount goal of the project, there is a huge speed penalty on ARM due to lack of virtualization instructions.