Here are a few, whether you consider all of them IF is a matter of judgment…
- Stories Untold - The first part is actually IF, but the other parts use computers or systems too, I think
- Her Story - You get a imitated PC desktop with a few apps, plus a keyword system though it’s overshadowed by the FMV clips
- Deus Ex Ceviche - by Tom Lento and Chandler Groover, some sort of fish and floppy disk thing, pretty complicated I think
- Arc Symphony - by Matilde Park and Penelope Evans, presents itself as a Usenet newsgroup
- Okinawa Online - My own game, made in Sugarcube…it has keyword-based navigation, similar to Her Story
- Quadrilateral Cowboy - A first-person game, definitely not interactive fiction—but you get a terminal with a full command line to work with and you can hack doors, gun turrets, cameras, etc.
Depending on how much similarity to a real GUI you want, Sugarcube for Twine is useful. As others have noted you can use text boxes to make a keyword system. I posted some simple code that does that here earlier this year.
You can also use Sugarcube’s dialog system to imitate pop ups or windows—albeit without drag and drop features like in a true desktop.