Apple's innovations are myriad and subtle, particularly on the software side. Almost all of these things have been copied by the various Linux environments:
- Sub-second reconnection to wifi when resuming from sleep, using past remembered networks and IPs
- Bonjour zero-configuration service discovery for printers, network speakers, etc.
- Exposé window management and the GPU-accelerated desktop in general, not to mention just-in-time-compiled GPU accelerated image and video manipulation with CoreImage / CoreVideo.
- Spotlight indexed desktop search that's actually usable for real world filetypes
- Quicklook instant previews, not to mention native PDF support not involving Adobe Reader
- A mail program that autoconfigures based on just the email address, just by trying the obvious options
etc
Add in the fact that Apple is still the only company to have multi-touch work properly on a desktop, that their hardware has been dominating geek conferences for years because of its travel-friendlyness, and there is plenty of innovation to go around.