Incidentally, if you are after specific examples, here are a few. Bear in mind that because they were done by Microsoft, who create a lot of "industry standard" applications, a lot of them are just accepted as standard.
I am not of the opinion that everything Microsoft makes is immediately rubbish, and I also don't bash them for no reason, and I do recognise a lot of positive things they have done.
1) With the introduction of IE4 and Win98 (and continued since), Microsoft took away the borders of buttons in some (but not all) toolbars and made them appear only when the pointer was over them. They also extended this "appearing border" to menus. This is immediately a bad idea; buttons should always appear as buttons, and act as so when pressed. This is common sense, but once again usability is sacrificed for the "cool" factor.
2) Since Office 97 (i think, maybe 2000), lesser-used menu items are removed from menus until they are "maximised" with a special button that appears at the base. This is to present new users with less options and reduce clutter. A good idea, you may think, until you realise that it "learns" which options you use most, and hides the rest. For someone who is not computer literate, menus suddenly changing their layout is a bad idea, and possibly confusing. Also bear in mind that the "maximise" button isn't necessarily obvious to a beginner, who might be reticent to click it, and assume an option is "lost" forever.
3) With IE 6, the picture view mode has special options that appear when the mouse is hovered over it. Besides the fact that these are buggy, and can leave trails when scrolling, all the options are ALREADY available from a simple context menu. These particular pop-ups are unlike any other pop-up i've seen in any other MS application.
4) Up until quite recently, quite a lot of Microsoft programs (Word being a good example) would have action buttons relevant to the whole dialog placed within the borders of a tab page. This is an unnecessary ambiguity that only serves to confuse. You could say "oh, but this was fixed with Windows 95", except that it was present in Word right up to at least Office '97!
There are loads more. I suggest you go take a look at the site :-D