The act of practicing difficult passages hasn't really changed through the ages (at least through my ages), but the tools to do it have. Faced with the huge task of preparing a program of difficult music (in my case a program for violin and piano), I'm using every tool I can get my hands on.
This is one way I use Finale to my best advantage. I'm sure it will work with other notation software programs.
I enter the piano part of a difficult section into Finale, and set a very slow tempo. Then I copy the passage twenty times (or as many times as I want to repeat it), leaving a measure of rest and then of just the pulse (played on some high or low note that has nothing to do with the passage) between each repetition. Then I go in and set incrementally faster tempos for each repetition. After the masterpiece is completed, I export it as an audio file, load it into my ipod, and let the passage "practice me." It beats pure metronome notching because you don't have stop to move the metronome, and you get the harmony and counterpoint notched into your brain along with the passage in question.