Like what applications? I'm picky about my applications too, it's not like I'm using Windows Media Player to view online content.
I would suspect any app that shows a web page (P2P apps typically have a page that shows you content from a web page) of using Windows to render content. An office document that shows on-line content is another possibility. It might be something completely unexpected like Winamp's window that pops up telling you that there's an update available, or Skype's window showing contact information, or "Windows Live Today". Perhaps a printer driver's window showing you offers on cartridges. Lots of things.
The only ones I think I would safely rule out that definitely show web page content are ones like iTunes, because I know that Apple developers would rather gnaw their own limbs off than use IE to render content
Think of it like this - if a software developer wants to show you a web page, and for some reason they want to do it as part of a window in their software rather than launching your default browser, why would they spend the time trying to render the content themselves or include a cut-down version of Firefox (like TomTomHOME does) to do the job. If the page they show you is their website, and it includes an advertising banner (or their site has been hacked cleverly), you just got owned.
Also factor in the amount of lame bits of software which are hard-coded to fire up IE even though it's not the default browser.
I don't know about you, but I've got better things to do than scrutinise the (non-optional) Windows Update list every time another load comes in. The last time that I got screwed by a Windows update was Office 2007 SP3, and that's because I had two versions of Access on my machine. Before that, I can't remember it ever happening, nor can I remember anyone I know having a problem with a Windows update, except for one guy who had a crappy Internet security suite which would block IE in its firewall config every time there was an IE security update. I replaced the security software when it did it on more than one occasion.
AFAIK the last time MS got caught trying to put on an update in an not-quite-100%-honest-reason was a .net framework plug-in for Firefox, listed as a critical update, but it rarely happens.