It has a nice clean interface and the letters are easy to input. Every cryptogram is a quotation, so you end up with (hopefully) something interesting to read at the end. However, this does mean that the quotations may have some long or unfamiliar words, but learning new words is also part of the fun! The one thing Cryptograms doesn't let you do is to see a full solution if you've given up on a particularly tough puzzle.
Hint: The way to get really fast solution times is to use the "Hint me!" button. Pressing it will show one correct vowel at a time - depending on the difficulty of the cryptogram it may show you 3, 4 or all 5 vowels. Thing is, it doesn't give you any time penalty for clicking it - so use it!
If you have a different favourite code-cracking website, then let everyone know in the comments below.