when you say encrypt a website, what do you mean?
are you talking about encrypting all of your pages, or just certain user/proprietary data that you store?
if you're just speaking to specific pieces of data then there are a few things to think about.
there are loads of encryption techniques at your disposal, some do a better job of certain actions than others. for example when you have a user login table you will probably want to hash the passwords to obfuscate them to view using something like SHA1. this is preferred to a full public/private key encryption (in this instance than other options) because it is theoretically more secure since hashes are a "one way" type of encryption. if someone gets a hold of your code base they still can't decrypt your passsword file, it is also faster on a login action to compare a hashed value to a hashed value than to do a full decryption of an encrypted value to compare the plain text.
now there are other types of data that you will want to do a full encrypt/decrypt with. a good use case to illustrate this would be if you store credit card information to allow the customer the ability to "quick reorder". then you would want to use something like Triple DES with a public/private key. this will allow you to store the number in a relatively secure manner (nothing is ever 100% secure), and decrypt it later when you need to send that number along with your order data to your processor.
so depending on what you're looking to do there are a myriad of different options and techniques that you can leverage to accomplish your goals. in specific reference to my example of credit card data there are even industry regulations from payment companies called PCI DSS (payment card industry data security standard) that outline best practices for not only how your code and algorithms should function, but also physical and access level security of your networks and hardware.
here are some general links to get your internal dialogue going:
*just a note to keep in mind. MD5 and AES are both considered broken at this point.
Code:
http://www.networkworld.com/columnists/2007/011707miliefsky.html
https://www.pcisecuritystandards.org/
http://www.15seconds.com/issue/000217.htm
http://en.wikipedia.org/wiki/Cryptographic_hash_function
http://en.wikipedia.org/wiki/Triple_DES
http://en.wikipedia.org/wiki/SHA_hash_functions
so give a little more detail on what you're trying to accomplish. i am far from an expert on encryption, but i would be willing to bet that there are plenty people on this board who are.