Gol D. Roger is the current holder of the title "Pirate King," and he also holds the highest bounty in all of One Piece. Currently, his bounty rests at 5,564,800,000. The second highest is that of his rival, Edward "Whitebeard" Newgate at 5,046,000,000. But it seems that the only reason his bounty is higher than anyone else's is simply because of his name.
When looking at the criminal history of Roger, there doesn't seem to be much to qualify him for the highest bounty of any pirate beyond being the King for conquering the Grand Line. In terms of strength, he and Whitebeard were pretty equal, with both captains and their crews fighting for three days and three nights before resulting in a stalemate. If nothing else, he and Roger should have an equal amount of bounty due to the fact that they were equal in strength. However, Whitebeard seems to have accomplished more in his time as a pirate than Roger did in terms of general piracy and accumulating crew members.
Roger seems to have accomplished few but grand things in his life. He conquered the Grand Line and began the Great Age of Piracy with his last words before being executed. He also learned the secret of the 'D' that many of the most powerful people in One Piece, including wannabe Pirate King, Monkey D. Luffy, have in their names. He, of course, fought against the Marines, with his main rival being Vice Admiral Monkey D. Garp. However, during the last year of his life, he was suffering from an incurable illness and was only able to reach the Grand Line thanks to Crocus' medical treatment. Had he not had Crocus with him, he probably would not have made it as far as he did.
Whitebeard, on the other hand, was able to conquer several islands and bring them into his territory, while ending slavery on at least one of those islands. He also commanded a fleet of 1,600 pirates. He brought stability and order to the islands in his territory and protected them from other pirates. Even during Roger's time as a pirate, Whitebeard was known as "the strongest man in the world." His strength was so immense that it was even greater than that of giants. He lived longer than Roger, so was able to cause more trouble for the Marines and build up his reputation. So why is there such a noticeable difference between the two men's bounties?
It seems it could come down to names alone. In Japanese, 6 is roku, 4 is yon or shi, and 8 is hachi or yattsu. Individually, they sound nothing like Gol or Roger. The key is that Japanese is made up of three different writing systems: kanji, the typical writing one sees in anime titles and character names; hiragana, the symbols that represent Japanese phonetically; katakana, which is a writing system used for foreign and certain other words. Certain sounds are the result of combining two phonemes, like putting together shi and ya to make jya. So, 6-4-8 is read as ro-shi-ya, or ro-jya--Roger. If we look at Whitebeard's bounty, we can see shi and ro (4 and 6), which when combined makes shiro 白, the word for "white."
That doesn't account for the extra 500,000,000, though. Therefore, the difference in bounties could simply be because Roger has "D" as his middle initial. It's known within the One Piece canon that anyone who has "D" in their name tends to be extremely powerful and "cause storms." The mystery surrounding "D" has been a lingering plot point for nearly the whole series, and few people know why it is such a big deal in the pirating world. The answers seem to lie on the island of Laugh Tale in the Grand Line.
All in all, when looking at why two pirating giants have been given unequal bounties, it seems that the main difference is that one just has an extra initial in his name.