No Audio Equalizer

MacOS has no built in way to adjust the bass and treble frequencies of sound coming from the system audio output.

Yes, inside iTunes, there is an equalizer, but if you want to adjust the audio frequencies of YouTube playback, for example, there is no way to do this.

This should be basic built-in functionality in any audio playback device, including a personal computer.

Right click

The right mouse button has been standard on Windows OS mice since 1995, and the "context menu" it displays is an integral part of the computing experience, saving time as well as educating the user about what commands are available for the currently selected object.

Apple refused for ten years to add a right-mouse function, and eventually enabled Control-clicking to display a context menu (a solution that is cumbersome, requires two hands, and is not Accessibility-friendly). Even so, in many contexts, no menu is available, as the concept is not a standard part of the MacOS user experience guidelines.

Forward delete

On Mac laptop keyboards, if you want to delete the character to the right of the insertion point, you must hold down the "Fn" key while clicking the Backspace key.

On Windows keyboards, the "Del" key deletes forward, and "Backspace" deletes back.

Manage folders in Open/Save dialog box

In MacOS, if you are saving a file and you realize that you need to to move/rename/delete other files, (for example, if an existing file's name conflicts with the name you want to save now,) you have to open a separate Finder window and do your file management there, then return to your saving task.

In Windows OS, you can rename, move, cut / copy / paste files and folders freely from within the Open and Save dialogs.

Single menu bar

In MacOS, there is only one menu bar visible at a time, at the top of the screen. This can be confusing, especially when you have an application focused, but it has no open windows. In that case, you might see another window showing through from a different application that is further behind, but the menu bar doesn't match.

In Windows, each application window has its own menu bar.

Update: You can use the MenuEverywhere utility to add a menubar to each window: http://www.binarybakery.com/menueverywhere.html

Can't resize from any edge of a window

In Windows OS, you can drag any corner of a window to resize the window.

In MacOS, you have to find the lower right corner of the window and can only resize in that direction. For many resize missions, this means you need to first move the window, then resize it, and then move it somewhere else.

Update: Mac OS X Lion finally adds the ability to resize windows from their edges.