If you just want to back up the wallet they are located in:
%appdata%\BitSwift
%appdata%\Stealthcoin
%appdata%\xc
and so on and so forth. In each of those directories, is a wallet.dat file (in the case of multibit, it's called multibit.wallet.dat). Just back that file up to a usb stick (or on your computer if it's a hot wallet).
If you're dealing with a lot of money, offline or paper wallets are the best for cold storage.
Multibit is slightly different to normal wallets. I would save all the files described in the post below.
I would go for an option very similiar to your (2).
a) Install MultiBit on your desktop, create a wallet (say it is called savings.wallet) and encrypt it.
b) Add however many receiving addresses you want for that wallet and label them.
c) Close MultiBit so that everything is written to disk.
d) You need to backup a minimum of the savings.wallet but I would go the extra mile and backup:
d1) savings.wallet
d2) savings.info
d3) the directory savings-data and all its contents.
e) Copy the files in d) to your three separate USB drives.
As long as you don't create new receiving addresses for your wallet, your backups will still be valid.
I suggest saving the extra savings.info and savings-data because then you will also keep your label information (in the info file) together with the automatic backups of the wallet/ private keys (in the savings-data).
You will also need your password to use your wallet, so you would want to keep that safe somewhere.
If at some time in the future your desktop wallet was lost/ stolen you can then go to any of the backup USB drives and simply open the savings.wallet in MultiBit. When you open the wallet it automatically syncs with the blockchain to get all the transactions and work out the balance.
Note that if you create NEW receiving addresses you will have to update your backups, as you have created new private keys in your wallet.
