Even if Windows is faster than Linux/FreeBSD during the first days after it has been installed, the registry, fragged disc clusters and added startup files will make the OS slower and slower until it one day simply hard locks. I'm currently using Gentoo on 4 comps and It's fast as hell with a stripped down kernel and only installed services. It's another story if you're using distros like Mandriva, Fedora, Ubuntu and so on. Their kernels are pre customized with extra drivers and they are often hogged with a lot of extra unneeded services.
Well that's one of the things I hate with Windows most; All the required maintainance which the OS needs is sick. You have to defrag your discs, clean the cache, clean the registry, defrag the registry, clean bad application entries. It's pretty necessary if you wan't to keep the OS fast and slim when using the computer a lot. It feels like MS have made the defragger deliberately slow because both OO Perfectdisc and Diskeeper blows it to mars and I haven't seen any big difference in performance with the inbuilt defragger during the past years. Is it really necessary to have like 5 extra third-party tools just keep the OS running? I smell some kind conspiracy/cartell...
In Gentoo I can't really think of anything similar that makes the OS get slower and slower. For me it has gone the other way after making all the optimizations and upgrading the apps + the kernel.
Spyware and viruses are also known to slow down the computer a lot. Sometimes they won't even let you in because of locking the comp just at the boot or login pre-login screen. Personally I haven't gotten any serious hijacks by viruses or spyware but It's been very close too. One day I just got enough after having to repeat that silly process at least once a week. If you still use Windows I and wan't to do like I did back in the Windows days, here's what I used:
Tuneup utilities 2004
Microsoft antispyware
Nod32
Windows update/Windows Auto update/Lose .exe updates
Diskeeper
Except these ones there were other tools that had to assist when some of these ones fails.