All computers have stalls. Even one windows install to another will have issues sometimes, it just seems random. However, being that the P4 has a longer pipeline than other chips like the C2D, Athlon XP, Athlon 64/X2 it is more prone to stalls if it's branch prediction fails. Basisically, it's a whole lot better at predictable things such as 3D rendering in Maya/3D studio, compressing audio and video, crunching numbers because of it's long pipeline.
But for stuff that is less algorithmically based it's more prone to being slower (games, things that require user input) so if you are comparing the performance of your PC to others that use different cpu's this is could be why. It usually won't create pauses so much as it will just slow performance down overall.
Other issues are definitely fragmentation of the harddisk, incorrect BIOS settings, or even programs you have running in the background or shoddy drivers that may not be releasing file handles after being closed for one reason or another.
The harddisk is usually the culprit as the speed limiting device of most of today's PC's. They're slow because they're mechanical and they slow with age because mechanical parts start to wear.
I would say use sysinternals autoruns and disable anything at startup that you really don't need and see if the system runs better. Hey it could even be spyware, so it's always good to do a Spybot + Adaware (or your favorite solution) check.
_ _ - - = = Pr3tty F1y = = - - _ _