What's hogging my machine for so long on startup?

The hard disk light being on fairly steadily does indeed mean that the computer is actively reading, and perhaps writing, to the hard disk at a fairly good clip. I agree with your suspicions that it's likely an anti-virus scan in progress. It turns out that's exactly what it is on my wife's computer .

In her case, I have the virus scan scheduled to happen in the middle of the night. Yes, we tend to leave our computers on all night, when backups can happen in addition to things like virus scans, without impacting our ability to use the computer. If, for some reason the computer was turned off over night, like when we're traveling, then immediately after boot the anti-virus software notices that a scan is over-due, and performs it immediately, slowing down the machine for some time.

That's kind of annoying. But, for what it's worth, we choose to live with it for now since, as I said, most of the time the machine is on 24 hours, and the scans happen in the wee hours of the night.

The solutions vary depending on the malware scanner you happen to use. For some "scan immediately if overdue" is an option that you can turn off in the scanner's scheduling options. For others, you may simply need to change the time of day that the scan should happen to be a time when the machine is more likely to be on, but not actually in use.

If none of those are options then getting into the habit of booting the machine about 15 minutes before you need it may be more practical. I have my machine automatically reboot overnight, so I login first thing in the morning when I get up, and then let it finish the login startup-sequence and download mail while I fix coffee and feed the dogs. By the time I'm done, it's done. And the dogs are happy.

Back to my wife's machine; even though I stated that we've elected to let it be, since it happens infrequently, I'm also planning to swap anti-virus software to a package that hopefully has slightly better scheduled / startup behavior. (She's currently running CA Anti-Virus.)

Now, to the more general question of identifying startup hogs.

I use a two pronged approach.

First, I installed Startup Delayer from r2 Studios. This lets me control which programs start when on startup, by inserting a delay for each. In a very practical sense you don't need everything right away when you boot, so by delaying when some things start up you often end up with a machine that's more usable more quickly. In your case, by spreading out the startup items over time you may be able to see empirically exactly which one it is that, when started, brings your system to its knees.

Startup Delayer can't delay everything, and some programs resist being delayed (in particular, the next time you take an update to that program you may find that the delay has been removed). But it's a useful tool, and allows you to take a backup snapshot before you start so you can restore to your original settings if you decide it's not worth the effort.

The other thing I do I've referred to as being very geeky, because I just do it for fun. I have Process Explorer in my auto-start. That means that every time I boot the machine Process Explorer is there fairly early and lets me watch what's happening.

Depending on exactly how and when your machine bogs down, it's possible that Process Explorer may come in too late, or you might not be able to click on the appropriate column heading to sort and have it respond in a timely manner. But most of the time it will, and I'm guessing that this will quickly help you identify your culprit.

To add Process Explorer to your startup, just create a shortcut for it in the Startup menu. (I have more detailed instructions in this article: How do I get something to open automatically when I log in to Windows?)