The primary syntax for the GNU assembler (GAS) is AT&T. Intel syntax is a relatively new addition to it. x86 assembly in the Linux kernel is in AT&T syntax. In the Linux world, it's the common syntax. In the MS world, Intel syntax is more common.
Personally, I hate AT&T syntax. There are plenty of free assemblers (NASM, YASM) along with GAS that support Intel syntax too, so there won't be any problems doing Intel syntax in Linux.
Beyond that, it's just a syntactic difference. The result of both will be the same x86 machine code.
