So much has changed since the beginning of the year that we decided to do a second run of our Builder Market Health Index to see where the top 100 home building markets rank as we head into the home stretch in 2009.

Rising unemployment, coupled with falling home prices and family incomes, conspired to add to the deterioration of housing market conditions throughout the country during the first nine months of the year. With the possible exception of Austin, Texas, virtually no housing market in the country is healthy today, at least not in a historical sense. In a classically healthy market, employment would be rising, along with home prices and incomes.

For this new list, we’ve introduced a Market Health Indicator score to gauge the relative health of the markets. A score of 50 or above indicates a healthy market.

As you can see from the list below, many of the markets that topped the list in February remain at the top in September. That’s the case even though the healthiest markets on our previous list, most of them in Texas or the Carolinas, were hit with rising job losses this year. Also, every major market in the country has seen falling median home prices during the last nine months. To take a look at the story we published in October on the 20 healthiest markets in our Fall list, click here.

For the Fall Index, we also improved the metric that we use to judge a market’s health. We now include data on household income. And, we broadened the reach of the list to include the top 100 markets (determined by building permit activity) instead of 75. That allowed us to include areas such as Madison, Wisc. (11) and Harrisburg, Pa. (72 ) this time around.

Several markets shot up in the rankings. Washington, D.C., where new home sales were up through September, rose from No. 10 to No. 3. The town of Colorado Springs, with its strong U.S. military presence, benefited from above-average growth in households, even as unemployment rose.

If you wish to see an even broader list of market rankings, Hanley Wood Market Intelligence, which compiled the data for us, sells a report that goes 200-markets deep. You can purchase that report by clicking here.

In the meantime, many of the markets that made our initial list of the weakest top housing markets in the country remain at the bottom. Here is a link to the weakest markets story that ran earlier this year.

And here is the new list of the 20 weakest markets in the top 100:

80. Gulfport-Biloxi, Miss.
82. Fayetteville, N.C.
83. Miami-Fort Lauderdale-Pompano Beach-Homestead, Fla.
84. Atlantic City, N.J.
85. Indianapolis-Carmel, Ind.
86. Winston-Salem, N.C.
87. Augusta-Richmond County, Ga.-S.C.
88. Syracuse, N.Y.
89. Vallejo-Fairfield, Calif.
90. Providence-New Bedford-Fall River, R.I.-Mass.
91. Bradenton-Sarasota-Venice, Fla.
92. Louisville-Jefferson County, Ky.-Ind.
93. Tampa-St. Petersburg-Clearwater, Fla.
94. St. Louis, Mo.-Ill.
95. Pittsburgh, Pa.
96. Memphis, Tenn., Miss., Ark.
97. Lakeland-Winter Haven, Fla.
98. Detroit-Warren-Livonia, Mich.
99. Clarksville, Tenn.-Ky.
100. Cleveland-Elyria-Mentor, Ohio
And here is the entire list of the top 100 markets for Fall 2009:

Boyce Thompson is editorial director of Builder.