3. Medicare costs and Social Security taxation

You might have to pay higher Medicare premiums or have your Social Security payments taxed if you do a Roth IRA conversion. That can happen if you are receiving these benefits and do a Roth conversion, Slott said.

"In general, Social Security benefits are excluded from the gross income of a taxpayer and are therefore not taxed," he said. "However, depending on how much other income an individual has, anywhere from 50% all the way up to 85% of their Social Security income can be included in gross income, resulting in a higher tax bill for that year."

What's more, he said, "Medicare Part B premiums are based on income. For 2010, joint taxpayers will remain at the lowest premium levels as long as they have income of $170,000 or less ($85,000 for those filing single). From there, premiums progressively increase until joint taxpayers have above $428,000 in income ($214,000 for those filing single). Conversion of a large IRA or plan balance could move you into a higher premium bracket, potentially costing a couple around $6,000 extra in Medicare premiums for 2010."

4. Financial aid loss

Most schools exclude a parent's retirement assets when considering a college student's eligibility for financial aid. "Income, on the other hand, is one item schools tend to look at intensely," Slott said. "And that's exactly what a Roth conversion creates. A Roth conversion will cause a spike in income for the year or years where the income is included. While this additional income is an aberration and does not represent typical income levels, it can cause a loss of valuable financial aid."

5. New Roth accounts need new beneficiary forms

The beneficiary form, according to Slott, is the most important estate-planning document when it comes to IRAs and Roth IRAs. It controls who ultimately gets the money in the account when you, the account owner, dies. Each custodian will have procedures in place for the conversion, but each new account you open will need to have the beneficiary forms completed properly and submitted.

6. Partial conversions involving after-tax money

When you have after-tax money in an IRA, you can't isolate the after-tax amounts and convert them tax-free while keeping the remaining pre-tax dollars in the traditional IRA, Slott wrote.