One Apple ID or Two?
You should have one AppleID per person that you use for iCloud, Notes, Contacts, Mail, Calendar and to-do's. You then pick one of these ID's to buy things in iTunes and the App store. You probably want to use the ID you have used to purchased music and apps with up until now.

So setup your wife's iDevice(s) with her new AppleID. When you are done, go into Settings/Store and change the AppleID you to your existing ID (only in the store).

Now you each have your own iCould but everything you buy can be shared between the both of you.