I've long favored Thomas, but the Dems have signaled a preference for Scalia. In other words, if Bush were to nominate Thomas, stand by for a bruising confirmation hearing and a filibuster.
The Institute for Justice (a libertarian public-interest law firm) has a somewhat dated, but probably still accurate, assessment of the Justices' records on individual liberties. Here's the bottom line:
Those ratings reflect IJ's assessment of the Justices' stance on IJ amicus cases and other major cases, in these categories: free speech and association, limiting federal power, property rights, race neutrality, and school choice. The main difference between Thomas and Scalia seems to lie in the realm of property rights, where both Scalia and Thomas are strong on takings but Scalia is soft on forfeiture. Kennedy places ahead of Scalia for the same reason.
Scalia would be a good second choice to Thomas. Kennedy is too much the compromiser on other issues.