If you have an application that was designed to run on SPARC, while one can usually migrate it over to Linux, it will take some effort to do so, as the applications that run on the systems are not binary-compatible. Because the architecture is completely different, your application will need to be recompiled. I prefer non-proprietary platforms. If you're developing a new system and the question is, which platform I would recommend you build on, I personally would develop on Linux unless your customers are mostly Sun folks.
I will say that there are advantages of using SPARC, such as the new UltraSparc architecture. They include energy efficiency, better fault tolerance and the cleaner architecture of RISC (big Endean). If your customers are large enough that they need optimum performance, availability and support, you certainly would not be making a mistake by going with a Sparc-based architecture.
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