A tip to start with: Windows (XP and Vista and Windows 7) know the concept of user accounts. And things like desktops and favorites are defined on a per user basis. So if your husband had used his own Windows account in stead of yours, it (this 'synchronizing') wouldn't have happened. After all, you can't expect iTunes to make a difference between HIS favorites and YOUR favorites in the same Windows account.
To recover, get them back from your backup. Some people (you might be one of them) find out too late that they shouldn't backup only their Documents, but some other bits and pieces of data elsewhere. Favorites are one of those.
If you had been using Firefox (in stead of Internet Explorer) you would have been lucky. Firefox makes an automatic backup each day. I'm not aware that I did anything to enable it, but I find 5 nice files in my [XP!] \Documents and Settings\<myusername>\Application Data\Mozilla\Firefox\Profiles\<myprofilenumber>.default\bookmarkbackups, such as bookmarks-2009-11-26.json (yesterday evening). Lovely. Although it doesn't really help in case of a hard disk crash or OS reload if it isn't copied to another medium. Still, it's a good start.
In IE you have to do this yourself via File>Import and Export ... To store the file, use a folder that is included in your regular backup. Or include the whole favorites folder (that's a folder called Favorites - language dependent - immediately 'below' your username) in that backup.
Yep, managing a PC isn't easy!
My husband just got an iphone, when he plugged it into my computer through my user it automatically downloaded all my internet favourites to his phone- I have A LOT of work related favs. after unplugging it he deleted my favs from his phone. Yesterday he plugged the phone back in to download his music. This morning when I switched my computer on ALL my favorites that he deleted from his phone have now been deleted from my computer...is there any way i can retrieve them???
My computer is a DELL hybrid running on Windows Vista and I use Windows Internet Explorer.