The System of the World, along with the previous two excellent books by Mr. Stephenson, ought to do a great deal to correct the injustice G. K. Chesterton perceived in how we think of Samuel Pepys:

Nine men out of ten in this country, above the most unlettered class,
could tell you with some confidence who Pepys was. He was a funny fellow who kept a Diary. He was a roguish fellow, and the fun of his Diary consists chiefly in his confessions of infidelity to a wife, or flirtations with a chambermaid. He wrote in quaint short sentences, often parodied in the newspapers; and he ended as many entries as possible with the phrase, "and so to bed". Now it is a very queer thing that this should be so universally known, and that nothing else about the same man should be known at all....Meanwhile, the rest of his life was a public life of practical usefulness and profound importance. He, with about one other man, made modern England a great naval power....His foes were the first men of the age, like Shaftesbury and Halifax; and they filled the streets with mobs of the Brisk Boys with the Green Ribbons, roaring for the blood of such servants of the Crown. And the roguish little fellow of the Diary stood up under that storm and steered like a ship the policy that has launched the ships of England. He fought for a fighting fleet, more or less of the modern model, exactly as Cobden fought for Free Trade or Gladstone for Home Rule.

--"And So To Bed", collected in The Spice of Life

UPDATE: The diary may be read here (which site Peculiar pointed out to me some time ago) in little snippets. The "cipher" Mr. Chesterton mentions was mostly just a system of shorthand, although Mr. Pepys also had a habit of throwing foreign languages into the mix when delicate subjects were... raised. I have been unable to find a decent online link to the shorthand system used, but I did, in my search, run across a neat notebook of Sir Isaac Newton. Which brings us back to the original topic of this post.