Remapping a Windows keyboard so that the key positions match a standard Mac keyboard is pretty easy.
Just open Keyboard Preferences, and click the Modifier Keys… button in the Keyboard tab.
This lets you change the behaviour of the keys on each attached keyboard (make sure you select your external one from the top drop-down menu).
To turn the Windows standard Ctrl⊞WinAlt configuration to the Mac standard controloptioncommand ⌘, just change the Option and Command drop downs so they have the opposite entries (i.e. Option performs Command and Command performs Option).
If you want to change the physical keys, most of the premium mechanical keyboards use Cherry switches that have interchangeable key caps. You can get Mac specific modifier key sets from places like DAS Keyboard and WASD Keyboards. If you want to go nuts, you can even get a fully customized key cap set in a style similar to Apple's keyboards, as this guy did (looks pretty nice IMO, but I'm sure it's costly).