Quantize should work directly on any and all selected clips by hitting the default key command Q or Alt+Q to Quantize 50%.
The Apply button is only for the Quantize toolbar, to apply any changes you've made there and it should be there. If you don't see it, try detaching the toolbar. It works as expected here in 2.65 for both audio and midi. Make sure that it's not set to "Quantize on Track", the right most small icon over the Apply button, which is a different function, but set as it is in the image below.
If you don't have the Apply button and quantize isn't working for you with the default commands, you might want to run the 2.65 installer again to see if the problem goes away.