Unfortunately, it looks like the repairwallet option was removed in 4.1.  You could sync up 4.0.0.5 again and run it from that client's console.  It will absolutely straighten out your wallet and find your coins.  Find a link to my bootstrap up a few posts if you need it.

If you want to do it tritonium's way and get your private keys:


If you've only ever used one address then go to console and type
dumpprivekey

If you used a bunch of addresses then
Go to console and type dumpwallet walletkey.txt
This will create a txt file called walletkey.txt in the directory you launched the client from with all your private keys.
It's going to dump a file with 100 public addresses / keys you can view in notepad.  
The one(s) you used that should have coins in them will have "label" next to the timestamp instead of "reserve=1".
Now, the question here is, since your wallet is a scrambled mess is this dump file going to be accurate in discerning addresses from reserves?
 
Now that you've got your key(s)
Exit the client and remove the old wallet.dat from the data directory.  A new one will be created when you relaunch the client.
Go back to console and type importprivkey .  
Wallet will lock up for a up to a few minutes while it imports the key.  
Any balances held in that private key will appear.
Problem with this method is if you have coins spread over several addresses this can get frustrating.