Okay - first, the 2-3 ms difference in access time will never be noticed by anyone - at least none of us. But it is
always preferable to isolate the OS on its own partition for one primary reason (and several additional reasons):
Main Reason: If you ever have to reformat you only lose the OS, not the installed Apps.
Why, do you ask, does this matter since you have to reinstall the apps anyway? Here's why:
1) Some apps (admittedly few, but some) do not install in the registry so they won't have to be reinstalled
2) Many apps keep user preferences in their own folders. They will remain intact even after a reinstall.
3) By having apps in separate directories, you have a built in roadmap of what has to be reinstalled and where - no need to keep separate notes.
4) Data Files. If you don't separate your data files (and of course you should), keeping apps on separate partitions does this for you. So if you lose the boot drive you don't lose your data (and you are backing that data up regularly anyway I know, but still....
).
5) Good housekeeping. Easier to find stuff if
you, not the Windows Installer, determine where it goes.
Yeah, MS says you'll take a minor performance hit in seek time if you use separate partitions. But as I said above I can guaranty it's nothing any of us would ever notice.