First of all, try cleaning up your machine:
1) Clean all temporary files (Disk Cleanup)
2) Defrag
3) Run Scandisk
4) Scan for virus' / spyware, as this can clog up your PC no end! Make sure the scanners are up to date!
I recommend this be done normally as general PC maintenance, just to keep your PC tidy and running smooth.
If it slowed down immdiately after you installed a new program, try uninstalling it again to see if that is the cause.
If you want to see what loads up on the system start up, go to run ("Windows key" + "R") and type "msconfig". Clicking on the "Startup" tab reveals all programs that load on boot. Try removing things such as notifyers and online update wizards, at least to try and find what's slowing the PC down. Be careful what you click in this program! If you don't know what it is, best to leave it alone! Also, create a System Restore Point before tweaking, just incase the worst happens! (I am NOT responsible for your mistakes, or what you do using this program!!!)
If there is still a problem, it is possible that there is a device conflict. If it started to slow down imediately after you added a device, try removing/uninstalling it.
I had a similar problem with my laptop (Acer Aspire 1501LMi), where the HDD took forever sometimes, but next to no time on other boots. This was due to Windows having 6 CRC errors when reading the HDD, and so set the drive from UDMA 5 to PIO mode. If you think this is the cause, I can recommend some sites on how to rectify the problem:
http://www.michna.com/kb/WxDMA.htm
http://support.microsoft.com/?kbid=817472
If you have any more information it would help a lot. I find slow start-ups tend to be common problem with Windows, but for many different reasons.
Tell me what effect this has, although hopefully it should help a bit.
Cheers!:P