Edit: other than iTunes
The App Store may offer things like the iCloud SDK but will restrict apps from using features that compete with Apples own apps, as well as any cool hacks which apps outside the App Store are free to make use of.
My take is that Apple is herding developers into the App Store, enticing them with SDK features and the promise of riches, and at some point they will change the default gatekeeper setting so that users see great big warning signs and are too scared of running non App Store software.
We're probably still a few years away from this happening, but the writing is on the wall.
So this is the only thing in my experience, that really sucks. The rest (compared to WIN) is really, really great.
I remember 5 years ago getting speakers to mute on my laptop when I plugged headphones in was impossible but I haven't seen a similar problem in my last few laptops.
For two monitors on one video card, things are pretty okay on Ubuntu and derivatives. More than that, especially 3+ with non-uniform geometries, and you will have fun. If you have multiple video cards, you will have even more fun.
Setup was pretty simple using the binary nVidia drivers on Kubuntu, 0 config file wrangling.
Now, having those three monitors in non-uniform geometries is something I wouldn't even consider tackling
[EDIT]
Kubuntu 12.04
All monitors in a single X Session and automatic application window sizing works as you would expect in KDE
(i.e. Maximising a window maximises to the current monitor only and being able to drag to right side of one monitor causes the window to use up half of the current monitor)
I ran Gentoo for years, and my experience was similar to yours. I could get things to work but it took a lot of frustrating trial and error, and then periodically a version upgrade would break everything and I'd get to start over. About a year and a half ago I finally got sick of it and installed Kubuntu.
Kubuntu 12.04 + 2 monitors + AMD proprietary drivers = you get to choose between accelerated OpenGL and multiple monitor support. You can't have both at the same time. (At least I couldn't, with the video card and driver versions I had 6 months ago. I spent many hours trying, then remembered I have more money than time and bought a $90 Nvidia card.)
Kubuntu 12.04 + 2 monitors + Nvidia proprietary drivers = easy. The GUI worked, first try, no problems. The only goofy thing was that my left monitor showed up on the right side, giving me a choice between physically moving the monitors or changing the default positions in the GUI. I changed the defaults in the GUI.
Also, on my former work machine, Kubuntu 11.04 and 12.04 + 2 Nvidia cards + 3 monitors = easy. (Some cow-orkers had 2 Nvidia cards and 4 monitors, also easy.)
I haven't tried newer versions of Kubuntu on a multi-monitor box, so it's possible (but not likely) they've gone backwards.
You could have switched the cables. Just saying :)
I did use xrandr to setup the virtual screen so that I could define the exact position of one screen relative to the other, which enabled objects to continue in an horizontal line across monitors.
The problem I run into with Linux is that sleep, suspend, and hibernate do not seem to work or work reliably. This is what is holding me back from jumping to Linux for the most part.
You know what Valve charges to put you on the Steam store? 30% or more. You know why some people do it? Because they make more money doing it. You know why some people don't? Because they make more money not doing it.
It's quite a pathetic situation when Mac developers have to resort to filing bug reports, yes bug reports, to try and address the issue of upgrade pricing.
Either way, I've alerted the committee of the Nobel Prize of Economics about your discovery.
The solution is simple.
All Mac developers should stop selling through the App Store, regain control of the distribution channel, and leave the Mac App Store barren of quality applications.
Until Mac developers have leverage, Apple will continue taking their 30% cut and enforcing rules which suit them and not the developers.
EDIT:
Just wanted to add...
What are developers going to do when Apple says every single new API in Mavericks can only be used if the app is sold through the Mac App Store? This has already happened with the iCloud SDK, so it's likely they will continue on this path.
What if one day Apple says you can only have a developer certificate if your apps are sold exclusively through the Mac App Store?