encrypt tutor
basically you don't have to use anything beside pen, paper and your head, although normally you will use notepad, to replace letters etc. It's hard to explain cause I myself am a newbie to the encr. But generally you have look for patterns, think what the hint means and how would you apply, also usually it's good to have for every challenge analphabet written down along with letters, like a=1… Also it's good to know about English, what is the most common word and colocation, the structure of sentence etc. Lastely usually it's good to start decrypting small words, because it's more likely that you will be able to presume what they mean
Look for a program called PolyCrypt. It's got a few neat functions that should help. My personal favorite allows you to put in the original text and to tell it to replace certain letters/characters with what you want. (Wow that was confusing).
Then again… that shouldn't be *that *hard to code on your own. I'm actually gonna get to work on making one right now, just for kicks.
Other than that, clone was right. Pencil and paper are your best bet.
Check out the official cryptography FAQ (the first 9 or so sections of it), and get ready for a lot of math.
Also, I touched on the subject briefly in some articles here. Feel free PM me if you have questions.
Of course that's all just broad theory. If you have a specific goal in mind, there are better answers.