I don't know what it is with the others here, I haven't met someone that doesn't know what you are talking about. There are many reasons for it, but some have not been identified.
I'll start with a better description for those that don't know. A fresh install of Windows will boot in under 1min. Over a period of 6 months the computer's boot time will not only slow but the entire experience of the OS is not on par with a clean slate. If you ever reinstall windows after 1 year of use you are sure to see the difference.
Reasons for the slow down have been attributed to increased clutter in your registry, and fragmentation of your disk. You have noticed that uninstalling does not help, this is in part because everything isn't cleaned from the registry. Ad-ware can be an issue, but this is usually not the cause.
You can get registry cleaners, defreg, and remove ad-ware, but even this will not return the system to its original speed, no one has come up with a reasonable explanation for this, it just is.
Note to others, this is not a normal behavior for an OS that is being used, I have been using Linux for 4 years, while this wasn't without re-installation, there had never been performance increase from a re-install or a slowdown from large amounts of installing/uninstalling programs.
1What is your timeframe? I assumed over months, others are assuming shorter. – None – 2008-11-20T16:09:48.223
I removed the not-programming-related tag because this is a big problem for Windows developers (has been for me, at least). – None – 2008-11-20T16:43:16.113
17My experience with vista is that it hasn't actually slowed down over time. I'm sitting on an 18 month install, and it's still just as slow as it was when I first installed it! – Orion Edwards – 2008-11-20T20:13:07.173
@Orion: Nice one! – None – 2008-11-20T20:25:11.517
3@MusiGenesis - It's a big problem for all people not just developers. You're starting down a slippery slope. This isn't a programming related question any more than the car you drive being related to programming. It gets you to your job, but that's about it. – George Stocker – 2008-11-21T12:29:48.357
@MusiGenesis: Not to mention you just closed a very similar question over here: http://stackoverflow.com/questions/308549/nt-kernel-system-process
– George Stocker – 2008-11-21T13:02:06.933Definitely programming related IMHO. – Agnel Kurian – 2009-05-21T05:02:28.917
Could changes to PATH and other environment variables be a contributing factor? – Agnel Kurian – 2009-05-21T05:06:07.807
2Should be moved to superuser.com, because it is not only relevant for programmers. – Mnementh – 2010-04-07T10:42:30.153
1I'm tempted to answer this question with one word - Adobe (things like Reader_sl.exe etc). – None – 2010-04-07T10:43:06.290
@Mne Agreed. This has got nothing to do with programming at all. – Yacoby – 2010-04-07T11:12:20.450
1After 6 months, Windows looses the will to live. – Trufa – 2011-03-01T14:43:30.387
FWIW, having a lot of fonts installed slows down Windows startup times quite a bit. Or at least it did on XP and earlier versions. I've learned this the hard way. – Joshua Carmody – 2011-06-01T18:30:13.110