With significant engineering talent focused on boot/prefetch optimization over the last decade, we've done thousands of hours of research on the subject. Early last decade, Diskeeper Corp did a great deal of work with Microsoft with regard to "sequencing" files for the prefetch technology built in to Windows XP and above.

More recently we've created boot optimization specific solutions such as HyperBoot that go beyond the performance available with Windows (e.g. Windows 7).

A key to improving boot up times is ensuring that files are in sequential order so that files can be accessed in order. This also entails that the files are not fragmented - at least the parts of the file required.

Several years ago, development work was done in the field of Linux boot optimization and was published in a report. It covers these points and the need to have contiguous blocks/files: 

You can read the report here.