I did this in one of my projects by writing a preprocessor extension to read the file version from my executable. So the WiX file looks something like:
<?define ProductName="$(fileVersion.ProductName($(var.MyApp.TargetPath)))" ?>
<?define CompanyName="$(fileVersion.CompanyName($(var.MyApp.TargetPath)))" ?>
<?define ProductVersion="$(fileVersion.ProductVersion($(var.MyApp.TargetPath)))" ?>
<Product
Id="<product ID>"
Name="$(var.ProductName)"
Version="$(var.ProductVersion)"
Manufacturer="$(var.CompanyName)"
Language="1033"
UpgradeCode="<upgrade code>">
I've posted the code for in on CodePlex: http://wixfileversionext.codeplex.com/