- The prefix centi- means 10-2. But while centimetre is common, I have never heard of a centiwatt or a centisecond.
- The prefix Mega- means 106. Hence Megabytes exist. So why do we not have Megametres?
All of the things you have mentioned exist, for exactly the reason you expect they should. If some are more common than others, it's likely because (a) only a few orders of magnitude apply to most kinds of measurement in everyday life and (b) most people are not scientists and, therefore, would rather say "a thousand kilometres" than "a megameter"... possibly because they don't even know what "mega" means.
By the by, isn't a megabyte equal to 1024 kilobytes (2^20 bytes), not 1000 kilobytes (10^6)? hah.
For scientists and engineers, the prefixes are defined by the International System of Units (SI). The exponents increase in steps of three.
(There is a link on the SI units page to IEC units used for computers)
Older MKS units like centi are no longer preferred.
[If you see a reference in the Jargon File to proposed units harpo- and groucho- remember, they were a joke.]