S Corporation Reform Act of 2006 - Amends Internal Revenue Code provisions relating to S corporations to: (1) allow nonresident aliens and individual retirement accounts to be S corporation shareholders; (2) revise S corporation eligibility rules to permit the issuance of preferred stock, remove certain restrictions on the issuance of convertible debt and S corporation passive investment income, and allow for adjustments to the stock basis resulting from S corporation charitable contributions; (3) revise tax treatment of certain S corporation stock losses and allow a tax deduction for loan interest incurred by an electing small business trust (ESBT) to acquire S corporation stock; (4) permit certain banks to qualify for an S corporation election; (5) set forth a rule for the tax treatment of the sale of an interest in a qualified S corporation subsidiary; (6) repeal the LIFO recapture tax with respect to S corporations; (7) extend the post-termination transition period for S corporations; (8) reduce tax rates on S corporation excess passive income; and (9) increase the cap on small issue bonds applicable to certain S corporation banks.