If you know that the source files will conform to standards, file extensions are unique to just about every language. I assume that you've already considered this and ruled it out based on some other information.
If you can't use file extensions, the best way would be to find the things between languages that are most different and use those to determine filetype. For example, for loop statement syntax won't vary much between languages, but package include statements should. If you have a file including java.util.*, then you know it's a java file.
