I have the same issue or concern. I think Misterboy is talking not about the program directory but the data directory as described here: https://en.bitcoin.it/wiki/Data_directory
Mine is over 300MB already, looks like the block chain files are the main culprit in the hundred of mb. Like the file blk0001.dat is over 300MB. But if I want to follow the instructions to secure my wallet here https://en.bitcoin.it/wiki/Securing_your_wallet
using a Truecrypt container it says to make the container at least 100MB. At this rate of growth it seems I need to make my container in the GBs if I don't want to keep recreating it? Am I missing something? Can I just encrypt a container for the wallet.dat and not the block chains?