Espionage does what you want. It costs 25 dollars, but it's pretty stable and does the job. You can choose which software you want to encrypt (and accompanying folders), and when you've set it all up, a password prompt will appear each time you want to open one or more of the programs you protected. Simply imput the password and you gain access. Once you quit a program, Espionage will lock it, so that when you want to regain access, you'll have to re-enter the password.
Here's the link:
http://www.taoeffect.com/espionage/