When I first installed the program I noticed that it was synchronising with the network, and whilst it was doing so it was downloading blocks. I wanted to know if these blocks will be saved on my hard drive or will be be deleted after the synchronising is complete. If the files are stored on my hard drive I wanted to know if when I uninstall the program will the files also be deleted?
The blocks will be stored on your hard drive in the application data directory. If you uninstall, the block files will be kept. There may be an option in the uninstaller that will remove them, but the wallet.dat file will be kept for certain.
Future versions of the mainline client, Bitcoin-Qt, will handle this storage differently via Simplified Payment Verification.