What is Tom?

Starting with the easy one I see!  Tom is a purposful enigma, and there are lots of theories, ranging from a manifestation of Eru himself (Tolkien denied it), one of the Valar (Aule has been suggested) or a Maiar spirit.  My money is on something a bit different, one of the Ainur of a different type to the Valar and Maiar, whose function is simply to observe and love Middle-earth rather than build it up.  The next best bet (IMO) is a nature spirit of some kind. There is an essay by Steuard Jensen that expands on this, called What is Tom Bombadil?, which is well worth reading.  There is actually no definitive answer, so you will have to choose for yourself, based on what you read.

Who created Orcs. Who created Uruk-Hai, Who created the Goblin Orcs of Moria

Strictly speaking, no-one (though ultimately Eru).  Morgoth corrupted existing beings, being unable to create incarnate self-aware creatures himself.  In the published Silmarillion he used captured Elves as his starting material for Orcs, but actually later changed this to Men.  For the full argument you need to read Morgoth's Ring, particularly the Debate of Andreth and Finrod, one of the most important essays in the History of Middle-earth in my opinion, and the section Myths Transformed.  In any case it was Sauron who perfected them, creating the Uruk-hai sometime in the Third Age, Sauron not Saruman as in the film that is.  Saruman seems to have created a hybrid race of Men and Orcs.  The Goblin Orcs of Moria are just one of the many races of Orc in Middle-earth.  When Sauron was defeated at the Battle of the Last Alliance many of them set up their own Kingdoms, particularly in the Misty Mountains, taking over the ancient halls of the Dwarves such as Kahazad-dum (later Moria), and Mount Gundabad, the most ancient home of the Longbeard Dwarves, in the North.  You meet, briefly, a Goblin King of the Misty Mountains in the Hobbit.

How many Elves really came to Helms Deep? Two, or an Army?

Only one, Legolas, Peter Jackson's film is very different from the books here.  In the books the Elves of Lothlorien and Northern Mirkwood (Legolas's home) have there own problems with Dol Guldur, a sort of mini Barad-dur in Southern Mirkwood.  The War of the Ring is much greater in the books than the film version, (good though that is)

Who created the Isitari

Eru created them before the world was made, they are in fact Mair, a junior branch of Ainur under the Valar.  They are in fact then a type of angelic being, putting on the appearence of old men, and there were five of them in the Northern parts of Middle-earth (in the essay nothing is said about anywhere else).  For more information there is an essay on the Istari in the Unfinished Tales, though when it was published Christopher Tolkien couldn't make out all his father's words.  He had another go later and the rest of the Istari essay s in The people's of Middle-earth.

Who rules the Hobbits?

They have a mayor, Will Whitfoot and later Sam Gamgee, in the books (Frodo became Deputy Mayor briefly).  The mayors are based in the 'capital' of the Shire, Michel Delving, but only exercise a limited power, presiding at banquets, and managing the Watch and the Postal Service.  The Mayors are elected every seven years, at a Free air on the White Downs at Midsummer.  The nearest they have to royalty among themselves is the Master of Buckland, a slightly seperate part of the Shire, and the Thain (or Took).  In the end Merry becomes the first, whilst Pippin becomes the second.  There is a bit more on this in the Prologue to the Fellowship of the Ring.  Ultimately though, they owe allegiance to the King of Arnor, the Northern realm.  Aragorn therefore will become their final ruler, but he grants them almost complete independence, with all three Hobbit offices as Mayor Counsellors of Arnor.