Just found this article and wanted to post it. I found this part quite interesting:
The NSA also has "major" problems with Truecrypt, a program for encrypting files on computers. Truecrypt's developers stopped their work on the program last May, prompting speculation about pressures from government agencies. A protocol called Off-the-Record (OTR) for encrypting instant messaging in an end-to-end encryption process also seems to cause the NSA major problems. Both are programs whose source code can be viewed, modified, shared and used by anyone. Experts agree it is far more difficult for intelligence agencies to manipulate open source software programs than many of the closed systems developed by companies like Apple and Microsoft. Since anyone can view free and open source software, it becomes difficult to insert secret back doors without it being noticed.