In no particular order, I give you my Windows and Microsoft annoyances. Trying not to favour another OS, and yes, I still use Windows.
File/Folder layout
Yup, this is a killer. Windows over the time has been built up of hack ontop of hack, and it’s file structure has changed several times, but with every change the older folders have been left for legacy applications. In OS X, GNU/Linux and BSD operating systems file locations are some what sensible. /etc for config files, /lib for libraries, /home for homes, /bin for binaries. It’s all placed in logical places.
Application Support files / Install
Windows has no single way to install and setup applications. Installers are not standardised and usually make a mess of the system. There is no one location for start up applications and every time you want to install or remove an application you must use a software vendors application, trusting them to clean up their mess.
Support files for applications are scattered throughout the system and it makes backing up a programs setting is fairly hard. It is slowly improving with Local Settings and Application Data, but still fair from perfect.
Standards
Microsoft can’t even follow their own standards, so how are developers meant to. Microsoft event’s a new standard for each problem they run into, and don’t even bother to look at existing standards to improve on.
EEE
Which brings me to my next point. The good old EEE – Embrace extend and extinguish. The wiki page explains it quite well, and even provides examples :>
DIrectX
Well fuck you DirectX.
Shell / Command Line
Oh dear god. The current standard shell is absolutely use, and has barely improved since DOS 6. Oh well, at least we have tab completion now. YAY! The good news is PowerShell is looking pretty cool. Shame PowerShell isn’t supported on Windows 2000.
Dodgy Virus Protection
Windows has protected once again. To slow down virus they have limited our connections and removed our telnet. It hasn’t stopped viruses, although it has annoyed the hell out of us.
Requirement to have a virii scanner
An operating system that suggests you run a virus scanner is flawed. All that should be required is security updates every several days, not a whole new product by a third party.
5000 versions of the same product (ultimate ect…)
Home Basic, Home Premium, Business, Business Premium, Ultimate. This makes maintaing computers an absolute bitch, and just silly. Provide one operating system for all computers. Eg OS X 
.
NTFS not being an open standard
This really isn’t a Windows annoyance, but an announce if you aren’t using Windows. NTFS standard needs to be open so other operating systems can read it.
Updates
Windows is excellent at updating every 3 hours, not to mention updating even when automatic updates has been turned off. This is quite annoying for me, and people that just want to turn off their computers. Instead they have to wait an hour just install a simple update.
Warning Messages
If you ever download an application on Windows Vista or 7, you’ll have just under 8 warning messages to click allow to, and due to this, all users become quite jaded towards the messages, and completely ignore them.
Unrelated Note
On an unrelated note, I would like to see Windows have a unified way to saving application data, and sandbox each applications. When applications want to use other applications data files the OS throws up a warning message asking if the program can have control over those files.
