Apple's biggest failures are that they abandoned open architecture when they introduced the Lisa and Mac which forced the Apple aftermarket to turn to the IBM PC and clones for sales. Apple's market share plummeted and the PC’s grandchildren are the worldwide standard.
With the Mac Apple failed to realize that they are not a hardware company. Some people might buy Macs because they are cute (at twice the price pf a comparably powerful PC), but most buy them for the operating system and software. If Apple would allow that software to run on other machines they'd make a killing.
Selling their own computers and OS has kept them at a solid 2% market share with no hope of improvement.
Apple has had a few innovations, but not many. They get far too much credit for things they didn’t invent or popularize (digital music, GUIs, etc.) but they do have a fanatical following and they should have more customers.
I say this, by the way, as an owner of just about every Apple product through the early Macs (except an Apple I and an original Lisa – anyone got one for me? :D)
Apple builds subtle tie-ins between software and hardware which would not be possible running on a generic box. For instance, with an Apple notebook computer, close the lid; the OS goes into sleep mode. Open the lid; the OS wakes. Tap the power button when the machine is already powered up; a dialog box appears asking if you want to shut down or put the machine into sleep mode.
Using the new Apple remote, you can wake the machine or put it into sleep mode via the remote. Handy if you are running a presentation or watching a DVD.