This was a great concept, and executed quite beautifully! I loved in particular how all the settings (the normal settings and the music) were blended into the desktop environment. It just made the game super cohesive--the entire game literally is taking place on this desktop.
The microgames were enjoyable--I loved having to close the spam windows at the same time as performing the microgame, and I also liked the Beardy interactions, although I think I personally would have liked the falling obstacles to be slightly harder to dodge, as they never really felt like a threat in my playthrough. That said, the times when he yoinked my game window were quite fun.
One UI issue I ran into: I initially completely did not pay attention to the file names, and so I figured "Endless" was just a name of some file I needed to clean up. Eventually I realized it really was an endless gameplay mode. At this point I tried to close the window, but the X buttons don't work (which I guess makes sense, because it would be annoying to accidentally close one--although that could be an interesting hazard!) Okay, so I figured I would just open one of the other files. At this point both the Endless file and one other file were open, and everything seemed to work. Eventually I did manage to lose in the Endless game, and so I was able to close the window. However, at this point, the spam windows stopped spawning and Beardy stopped attacking. And then, what seems to have happened is I won the 10 microgames that I needed to, but then the window just didn't actually get completed, and I had to re-play it again, and at that point the spam windows and Beardy started working again.
So it seems like there are possibly some bugs happening there. One possible UI improvement I can think of--enable the close button when two files are open? Or maybe instead of a close button, have a minimize button, that paused that file (so the next time you opened it, you would be back where you left off). I don't know, some things to consider.
One other thought I had: I think it would be cool to have some more particles/animations, e.g. when blowing up the viruses in the shooting game, or collecting them in the collecting game, etc. This could just slightly improve the game feel. That said, the "instant despawning" effect does fit the overall aesthetic of the rest of the game.
Overall, I had a great time with this. It was a lot of fun playing with the different features on the computer, and the core microgame gameplay was really good as well.