All of these are nice, and contribute to my enjoyment of Linux.
But, there's one thing that always makes me reboot from Windows into Linux (if I was gaming or watching Netflix; I usually run Linux): Having to do any work involving the command line, whether local work such as development, or remote work such as building and deploying packages or website updates.
PuTTY isn't a bad ssh client...but, it's not the same as always having a bunch of gnome terminals open in tabs and being able to "ssh myserver" or "vim myprogram" or whatever I need to do. The mental friction of having to click through menus to open a new ssh session for every server I need to work on (I've usually got two servers open when working: staging and production; and I've often got three or for sessions per server). Sure, I could use screen or tmux, but I can't remember the key combinations. And with gnome terminal tabs I don't have to. Worse, PuTTY doesn't seem to support the keepalive functions that OpenSSH does. I can keep my ssh sessions open all damned day under Linux. Under Windows, if I walk away for lunch or a nap, I have to relog everything when I get back.
Not having them in tabs, and not being able to manage windows under Windows in any reasonable fashion is also frustrating. It's an exercise in frustration finding the right terminal (there will always be two or three with the same label, unless I explicitly make an effort to change it; with tabs I can put them in the order I always use and know exactly where everything is without reading; windows get moved around all the time).
Lack of middle mouse button paste was always a nuisance until I got an awful HP Envy 15 lappy without a middle mouse button...it has the Mac style single mouse button with click areas, which never work right, in Windows or Linux--I often get a right click when I wanted left and vice versa...I've had to retrain myself to use three finger click, which is error prone and I end up getting a double paste....basically I'm realizing that I've been living in misery ever since I got this awful laptop. I need to order a bloody mouse, so I can stop punishing myself with this clickforsaken thing.
Actually, there's a ton of things that are coming to mind now that are just an awful nuisance. Lack of a good command line is the biggest. I use locate and find all the time; the analogs on Windows are a joke. grep! sed/awk/perl for munging things quickly! cygwin is a second class citizen and I'm always trying to figure out where I need to go to do what I need; the paths are so weird and long. That can be said of Mac OS X, as well, to some degree...while it has an actual UNIX underneath, it still has all the clunky Mac baggage that makes it ornery.