I don't mind proprietary software. Really, I don't. I don't mind that Apple makes all its software proprietary at all, nor that one can only use Apple software on Apple hardware.

I just really, REALLY hate that I need iTunes installed to do f-all with an iPod or iPhone. Why? Why do that? I already HAVE a media player AND a file manager on my computer, and I can already buy music off the internet with a web-browser, so why make me use iTunes when it doesn't do anything any more efficiently than all these other applications (admittedly, the online music shopping experience is a bit lacking)?
I hate that it does all sorts of weird and wonderful things to your iPod/iPhone if you dare plug it in to more than one computer. Why can't my PC recognize my iPhone any more? It's since I plugged it into that Mac, isn't it? Look, I'm not having an affair or anything, you don't need to get so upset - it's just that I have to work with Macs at college. I JUST WANT MY MUSIC BACK, OK?!
I hate that iChat isn't compatible with anything but itself. If it worked with XMMP, then at least I'd be able to contact my Mac-using friends with Google Chat, but no! I have to spend upwards of ?1000 before I can send a, "hi" to someone. That, or I can spend sweet F-A on Skype and still contact them, but that's not the point.
I hate that my screen can display millions of colours, so many colours in fact that I can't tell where one starts and another ends, across billions of pixels on that gorgeous display... but I only have a choice of 2 colour schemes. Come on, man, that's just really, REALLY lame.
I hate that I can't keep everything nice and organized, in folders that seem natural, and still access frequently-used stuff on my desktop. So what, my coursework needs to be either in my Documents folder or my Desktop? I can't just link to Documents/Coursework from my desktop? Yes, I know I can do, "ln -s Documents/Coursework Desktop", but I can't believe I can't do the same with a simple click-and-drag. Give me a break!
I guess I also really hate that it's not as simple as a patch and a recompile to get what I want, but that I have to hope that Apple sees these things as significant enough to fix/change and then pump out another release of their OS. I'm not holding my breath, obviously.

That said, there are a lot of good things about Apple products, and I certainly wouldn't hesitate in buying some of them for someone else or giving an unbiased point of view to someone. These are just things that annoy me, on varying levels of seriousness. Of course, what I use (KDE SC 4.4 RC2 on Kubuntu) is far from perfect.