Chis started his generator in his apartment back in 2000, with names culled from Tolkien's work by a friend of his, Jane Pinkard. 
Eventually he also started an Elven generator an the same principles, which we will review in another article. His Hobbit name generator is probably the most well know hobbit name generator. His names are genuinely Tolkien based, and although it might be possible for the generator to come up with a complete full name which Tolkien already used for someone well known, it is easy enough to plug in a name beginning or ending in a single different letter to give you a result that isn't already in use by a famous character.
Another Hobbit Name Generator is at the site Sport Generator, and seems to be provided by the Swami's Name Generators. He also has a Female Hobbit name Generator.
The Male Hobbit Name Generator
Here, I find Henry Johnson gives me Holfast Bunce, Milo Bracegirdle-Chubb and Hamson Goold-Brownlock; Harry Jones becomes 
Bingo Puddifoot-Oldbuck, Samwise Fallohide-Sandyman and Otho Grubb, Finally, Harry Johnson generates Orgulas Twofoot, Hal Took and Peregrin Baggins. These are obviously not mapping to anything as straightforward as the Secret Name Hobbit name generator, and this allows you to repeat you name as a entry until the generator comes up with a name you fancy.
The Swami's Female Hobbit Name Generator also seems to use the same principles. I enter Rebecca Scudder: and receive Amaranth Twofoot, Peony Goldworthy and Esmerelda Sackville. This time Robyn Snyder becomes Angelica Mugwort, Asphodel Bunce and 
Prinula Fallohide. I try Nancy James and the generator gives her Mimosa Sandyman, Merimae Took and Rose Bolger. Again, you can repeat your name until you find a hobbit name you are comfortable with.
The author of the generator has a couple of notes for users;
You may have noticed that there are three distinct kinds of first-names generated here: First there are "regular names", such as Baggins, Frodo, and Lobelia, like those found in the world [of the third age] today. Second are names connected with nature, such as Rosy, Tunnelly, and Longhole. These are often names from the Eastfarthing, especially the area around Bree, and thus sound different from the others. Last, there are archaic names, such as Mirabella, Gorhendad, and Canellia. These are often the names of Hobbits from long before the time-period of Lord of the Rings and are often in the style of Men.
The autho
r also says:
If you have tried out both this page and the Female Hobbit Name Generator, you may have noticed that the male names repeat themselves much less often than the female ones. This is simply due to the quantity of male names Tolkien created versus the number of female ones. Lord of the Rings is a very male-centric series (all nine members of the Fellowship are male), and thus there are many more male names than there are female names.
This may be true with a large sampling, but the nine times I tried for female names, I did not have a repeat with either the first name or surname.