It looks like haibanerakka was right: the Troubled Windows Flash animation is the OS Girls. It's not a real series, just a bunch of talented and somewhat twisted artists from the Japanese imagepost site Futaba Channel. The OS Girls ("ＯＳたん", using the cutesy childlike pronunciation of the suffix "ちゃん") are mascots for various OSes, and their appearances are based on the common impression of the OSes: Windows ME is frustrating and prone to crashing, so Mi-tan (the green-haired one) is eager to please but clumsy; Windows 2000 Professional is considered more stable and trustworthy, so 2000-tan (the one with short blue hair and glasses) has a more serious look, and since 2000 and ME came out around the same time, she is Mi-tan's guardian; XP is pretty but bloated and slow, so XP-tan is cute, busty and not too bright. The freaky doctor guy is Dr. Norton (Norton Antivirus). Wikipedia has more information. There are a bunch of pictures from Futaba Channel here; most non-worksafe images are in the "adult" (アダルト保管庫) section, but the Japanese have somewhat different standards of what is "adult", so caveat clicktor. They even have more Flash animations (my favorite, besides the anime intro, is OS-pittan).
Some people from 4chan have apparently translated some Troubled Windows fan-comics, but the site seems to be down.