NOT in order of annoyingness:
Quicktime - It's both a terrible media player and it is insanely unwilling to be removed. Apple's central design concept seems to be preventing the user from doing what he wants. If I delete qttask.exe, it means I don't want that file anymore, not that I want it to be resurrected. If I disable it in msconfig, it doesn't mean that the next time Quicktime runs I want it to get a new startup entry.
iTunes - ituneshelper.exe is about the same as qttask, and iTunes is even worse at playing music than Quicktime is at playing movies. It's the single most bloated piece of software I've ever used. The iTunes store is another reason to avoid it, not to use it. It also crashes way too much on a new MacBook Pro, and since I don't know what Apple compatible software is a good replacement for it, I can't just replace it for my friend as I would if he had Windows.
Apple Updater - Everyone I know just installed Safari. They didn't mean to.
Flash - Thank you, Flashblock, for making the internet useable again. Thank you, bad web designers, for sticking retarded flash "intro pages" on your sites so I can see that they've been blocked and then avoid your company on principal.
HP Printer Philosophy - Thanks to you, too, HP, for making a printer that needs an IP to be set via a web interface in order to access that same web interface. Thanks to my neighbor for having a parallel cable sitting around so I could access it in a more traditional way.
Windows Desktop - Why do you lose my icon placement every time your resolution changes? Luckily, there are countless little freeware apps to save icon positions.
Real Player - You basically invented the Apple "if you uninstall me but I will grow more powerful than you can possibly imagine" routine, so you get extra evil points for originality.
Logitech Mouse Drivers - My mouse drivers are now 100 megs. Finally they fixed the two year problem of needing to run them manually after booting (running on startup caused them to fail), but they still involve two separate taskbar icons and take up a ton of RAM.
Word - I know how to make you do what I want, but it took years to learn how to both stop your autoformatting and then put in the formatting I want. I hate the way you place images. I hate the way you resize my stuff after I've already locked it down.
Verizon Phone UI - My phone had a great UI and lots of nice capabilities when it was made. You removed bluetooth file transfers so I'd have to pay you to get photos off my phone, and you made the interface ugly. You removed the ability to vibrate and ring at the same time. I'm glad my phone was so easily hackable.
Flash (again, but bear with me) movie players - The only reason you exist is to keep me from saving video to my hard disk. Guess what. I can still do it. Meanwhile, you're slow, often not resizable without using a magnifying tool to manually zoom onto your little box, and you require me to enable flash.
I know how to fix or replace all of you, but you kill me every time I have to use a new PC and wade through your bloated code again.