I recently worked on an HP Media Center tower with good specs that shipped with Vista preinstalled (Athlon X2 6000+, 3GB RAM, GeForce 8500GT, 2 x 500GB SATA 3.0 Gbps drives).
I previously did all the maintenance that could be done; ran disk check with surface scan and file system repair, defragged, cleaned up all temp directories/files, removed a few unwanted programs, scanned for viruses/malware (none were found), updated drivers, patched Windows with the latest updates. It still had laggy issues when booting or launching apps. Even GUI stuff like dragging and dropping icons would have a big lag or delay.
So finally I wiped the SOB and clean installed Vista SP2 OEM from my System Builder disc (I used Vista
Activation Backup and Restore to preserve the OEM activation). Installed the latest drivers, only the apps and utilities the owner actually wanted/used, updated all apps and Windows with the latest patches.
The owner said it was like a brand new computer - it runs better now than it ever has including the day they bought it (two years ago). I've seen this dozens and dozens of times. I'm not certain how the OEMs build their factory install images, but whatever they do, it can leave the software environment hopelessly dysfunctional. Sometimes, you just have to wipe the drive and start clean.