Every 100 transactions, the official client (that I use) will create a bunch of new addresses, that will not be included in a former backup of the wallet.
But normally, you should never send any coins to one of your address that is not backed up in a way or another.
And I don't understand at which moment you have the possibility to backup these new addresses? Too early, they are not created yet. Too late, the hard drive could die before you make any copy of it.
A possible solution is that the new addresses are created before they are actually needed (say, created at transactions 95, but actually used only from transaction 100), is that how it is implemented?
I assume you are asking about the Bitcoin-Qt wallet?
If so, then the wallet creates a new address each time it uses one of the old addresses. In this way, there is always a queue of 100 unused addresses.
So:
If you create a backup, and then use 25 addresses, the queue of pre-generated addresses will have 75 addresses that are in your previous backup, and 25 new addresses that aren't.
If you then create a new backup and use another 25 addresses after that, the queue of pre-generated addresses will have 50 addresses that are in both backups, another 25 addresses that are only in the second backup, and 25 new addresses that aren't yet in any backup.
