Yes, even as something as simple as a fluctuation in power can expose the difference between a more expensive workstation and a cheap PC.  I can recall many times when the power in the building has surged (eg during a storm), and all the cheap PCs have rebooted but all the Macs have stayed up - I'd suggest that the crappy power supply is the biggest liability in a budget PC rig.  But obviously not all windows machines are cheap and nasty.  One company I worked at (many years ago!) used Alienware PCs as workstations, they were rock solid and beautifully engineered inside, but they weren't cheaper than a Mac.  The HP workstations are really nice.

But once you're up and running After Effects - or any Adobe software - you really can't tell what OS you're on and it doesn't make much difference.  It's when you run software that isn't cross-platform that you have issues.  Post-houses that rely on Final Cut will be stuck with Apple, those that rely on 3D Studio Max will be stuck on Windows.  At least Maya and Nuke give you the luxury of choice...

-Chris