Reclaiming disk space describes what is nowadays called pruning. After downloading the entire block chain, you can safely throw most of it away because old spent transaction outputs are never needed again. This is not yet fully supported in Bitcoin Core, but it probably will be possible in the next major release.
From the paper (my emphasis):
Once the latest transaction in a coin is buried under enough blocks, the spent transactions before it can be discarded to save disk space
You're talking about simplified payment verification (SPV), the next section in the paper. With SPV, you use just headers and Merkle trees to verify that a transaction has a certain number of confirmations. A transaction with a high number of confirmations is probably safe, but you can't be 100% sure without downloading and verifying the entire block chain. SPV clients trust that the majority of miners are honest, which full nodes do not need to do in most cases. Today, SPV is used by many lightweight clients such as MultiBit and Bitcoin Wallet for Android.
Thanks Greg that's what I figured. I was missing/forgot the part that transaction depend entirely on the balance of other past transactions. Nonetheless, using the Merkle Root in the headers you can still verify if a specific transaction exists in a block. So you could validate the set of new transactions this way no? – Luca Matteis – 2014-09-04T07:13:51.590
@LucaMatteis How could you verify that there didn't exist a transaction that spent those funds unless you either check every transaction or maintain a table of all unspent outputs? – David Schwartz – 2014-09-04T21:13:04.017
@DavidSchwartz so with the Merkle Root you can only verify that a transaction is part of that block but you can't verify that enough funds are available, right? – Luca Matteis – 2014-09-05T14:03:34.007
@LucaMatteis Assuming you mean this, you are correct: "You can verify that the past transactions that a new transaction depends on were part of a block, but you can't verify that the funds the new transaction uses weren't consumed by some other past transaction." – David Schwartz – 2014-09-05T15:38:36.993