Malware now infesting my primary computer:

I run Ubuntu Linux (10.04, so I've got until April 2013 before I have to find an alternative), and am reasonably secure I think. So I don't think I've got any malware installed. Though Firefox has been crashing regularly since I updated to 14...
I don't have Adobe Flash, or Adobe Acrobat Reader, or any Adobe products on my machine. I do have MS Windows 2003 in a virtual machine, but rarely run it. I also only run software from the repositories (and only Free Software) rather than randomly downloading stuff from the 'net. I am also careful with my browsing habits, using NoScript and RequestPolicy (which, once set up, are surprisingly painless, esp. NoScript) for example.

Seriously though, there are three (and more!) great reasons why Linux based systems are inherently superior to MS Windows.
1) Lower usage by people who mindlessly click through things, leads to fewer bad peeps targeting the OS.
2) A wide variety of variation (not just in distribution, but also CPU-type, etc.) means that it is much harder to target with malware (though this also makes it harder for other proprietary systems to run, I don't really give a shit).
3) Even if you do get access to a Linux based system, the security model makes it easier to clean up afterwards (as all you have to do in most cases is just delete the user account and files that were infected).

Of course, Android is an example of a Linux based system that demonstrates that I'm not correct with at least the first point, and probably the other two points as well.

1. Don't fuck with Windows Services. They're set that way for a reason. And no, I don't give two shits about some Windows optimization guide. Six months later, something wont work right and you'll end up chasing your tail only to figure out it's because of something you did six months ago and completely forgot about it. Trust me, I've seen plenty of "PC gamer" type people trip over themselves plenty of times doing this kinda crap.

2. The default time for Windows Updates to install is 3AM. A reasonable time for most people. But if you insist on working/playing at that time, sure, change it.

I'm glad you asked. As far as I'm concerned, taskbar blinking is more than enough for me. At most (and this should be configurable), a small corner overlay rectangle with first few words of incoming text should appear, but without stealing focus.
Horrible behavior which needs to be avoided and Yahoo Messenger does it plenty:
- If you lose Internet connection and it comes back, re-connection to the server should transparently happen in the background. No pop-ups, no warnings, no focus stealing once reconnected. Yahoo messenger has this bad habit of having its main window appear on top of everything else after it reconnects, even if previous state was "minimized to system tray". It's simply great when it does that at 1 AM, while you are watching a movie and holding your asleep baby in your lap. Really helpful!
- If someone starts chatting with you, see above: NOT nice to construct the window on top, especially if my status is "Invisible to all" or "Do not Disturb".
Bottom line: don't put window on top, with or without focus stealing, when someone starts a chat, because there's no reliable way to know what the user is doing. Maybe they're presenting some report to a VP and the last thing they need is a "'sup, dude!" from buddy Joe, or even worse, some stupid/obnoxious/racy pic from Uncle Skuggle. Yeah, I know, the user should have closed all chat software and whatnot, but sometimes they forget. Point is, YOUR application should be discreet unless otherwise specifically configured.

boot to a live distro and dismount any HDs or removable media works ok