The new "qualified use" provision means that many people will have to pay taxes on at least a portion of their capital gain when a house is sold. Exactly how much will be something an accountant will have to figure out and the figure will be different for each tax return. The blanked $250,000 and $500,000 exemptions are history.
As I understand the new law, the provision of the old law will remain in effect until January 2009. After that, each unoccupied month will count against "qualified use." Since you will have 9 years and 2 months under the old law, your tax liability will grow slowly. If the house does not sell until January of 2010, for instance, you would have 12 months of non-qualified use and 110 months of use under the old law, so 12/122 or 9.8 percent of your gain for the entire period would be taxable.
This is the most aggressive interpretation of the law. If you counted 10/99 through 12/06 as your qualified use and 1/07 through 1/2010 as non-qualified use, the ratio of non-qualified use to qualified use would be 36/122 or 29.5 percent.
As a practical matter, this law actually benefits you. Under the old law you would lose your tax-exemption when you had not occupied the property in 2 of the preceding 5 years. That means every dime of gain would be taxable on any sale after 12/08. Because you have owned the property for a relatively long time, you'll be taxed on only a small portion of the gain after 12/08.
Scott