Because I have a full sized tower I have it on the bottom shelf of my desk. It's actually so big that I had to remove the sliding keyboard part of my desk since the PC tower has a weird strange angle to it that would hit that sliding keyboard part. So Instead of removing the top of the tower the keyboard thing had to go.
I do keep stuff on top of my desk though, until the last 2 months I kept both my Xbox 360 and PS4 on top of my desk, but now that I have a PS5 and XSX, I have the PS5 at the top of my desk because of its width and I keep the XSX on the bottom near my PC tower.
Another good reason why I have it like this is because I have a lot of physical PS4 games and it's just a lot easier to insert them like this compared to my XSX, where I don't really have any physical Xbox games and plan to play mostly digital stuff. The other issue is that I would use the XSX for multi media stuff but I switched over to the PS5 since I ended up purchasing the multi media remote for it. What are some good XSX multi media remotes?
Even though there is no need for it, I would like to at some point to install a 4K Blu-ray drive into my PC. I use to have a Windows multi media HP remote and IR sensor but I threw that out years ago not thing about how useful that might actually be.
Even if I got a newer bigger deal I would still keep the PC tower in the bottom shelf, I've even seen some pictures of people with ATX towers that are on the top shelf above their monitor, that just doesn't seem safe especially since they have a glass side panel.