The dirty fuel filter just keeps fuel from getting that far, and is normally noticed by feeling like you are out of fuel at high rpm's.
Clogged injectors are from residuals in the fuel, or poor fuel. There are excellent additives to clean. Some companies pay the little extra to put it in the fuel (Chevron), and sell it separately for those who shop for the cheap gas (unfortunately those are the same people who don't believe in fuel additives or try the sheap ones and condem them all).
Bob has an excellent example here of how diesel deposits form and the advantages of diesel conditioners that can be extremely effective (some of them). While that study is a laboratory one, I have seen the results in engines and exhaust.
