I'll start this by saying I am not an accountant or a tax specialist, if you are unsure of what to do the best advice is to take some of your iPhone earnings and get some real tax advice. ; )
What I am is an iPhone developer who made a sizable amount from the app store in 2008 and I just did my taxes this week.
I am registered with Apple as an individual. I assume that if you registered as a company, then you already own a company and should know what you are doing in terms of taxes.
As an individual, you will not receive a 1099 for any of the money you have earned from Apple, nor will Apple report any of your earnings to the government (at least for US Store earnings). This means the responsibility is in your hands to claim your earnings. Like an above poster stated, this is directly from Apple's mouth. Here is what they told me word for word:
Since the App Store contracts are characterized as a "sales/commission" agreement, as opposed to a "royalty" agreement, there will be no tax withholding or reporting in the United States.
In addition, payments from the USA App Store will not be reported to the IRS on form 1099 or 1042 at year end, so you are responsible for reporting your own taxes.
Don't take this as an opportunity to try to cheat your taxes, doing so could land you in some very hot water. Also, by the wording sent to me from Apple they may be reporting all your international income.
Personally I used TurboTax to file my taxes, it made things pretty easy and helped me understand what I could and could not deduct. In the end what you will need to file is 1040 Schedule C (Profit or Loss From Business) and a Schedule SE (Self-Employment Tax). Whether or not you have formed an entity like an LLC or not, the government still considers you to be a business when you earn income like this. On the Schedule C you will report all your income from your iTunes sales, and you will also get a chance to deduct related costs of doing your iPhone development.
As far as how much you will have to pay in taxes, mileage will vary from person to person. Basically you will have to pay the federal and state taxes based on your income bracket, plus self employment tax (social security + medicare) which is an additional 15% or so.
Going forward in to 2009 you may need to start paying estimated taxes each quarter if you are making large profits. The IRS doesn't like you holding on to large sums of tax on your own if you are making a lot of money. I know there are penalties involved at some point, but I don't know the specifics. Better safe than sorry.