I think that what confuses people is that they equate Apple ID with iCloud account (formally MobileMe account.) They are not the same!
An Apple ID can be registered with any email account, be it an @me.com account, a @hotmail.com account, an @gmail.com account or any other email account. My Apple ID is registered using the email address that I have using my own private domain name.
An iCloud account (what was previously a MobileMe account) is an account that is used for gaining an email account and other additional service associated with iCloud. It is like similar to registering for a Gmail account or a Hotmail account.
Generally, what you should have is one Apple ID that is used as an iTunes Store account. That one should be used by everyone on their various devices and on their Mac/PCs in iTunes. This way all purchases made in the iTunes Store, be they apps or other media, can be shared by everyone.
As for iCloud accounts, these should be separate and unique for each person. They would use the same account for each of their personal devices. This will give each person separate accounts for email, iMessage, calendars, etc.
If you already have an Apple ID that you've been using in iTunes as a store account you should continue to use that for all purchases. In addition to that you should register separate iCloud accounts for each person who needs one so that they have separate IDs that can be used for email and messaging.