>>Nancy,
>>
>>I think E. B. would say that it's acceptable to put punctuation outside of quotation marks in the rare case when it is necessary to the substance of the sentence. In this case, it's important to differentiate between the user entering "Thoma" or "Thoma."
>>
>>>I'm in a grammar quandry. Good grammar would have me write:
>>>
>>>...you could enter "Thoma." But the _word_ is "Thoma" so I think I should write "Thoma". But the ghost of my 6th grade english teacher (Miss Fisk) keeps whacking me on the head.
>>>
>>>I know: this is totally unimportant. < shrug >
>

From the Chicago Manual of Style, 14th ed., rule 5.87 (the example is theirs, not mine):

In close textual studies and on similar rare occasions when the inclusion of a comma inside the closing quotation mark may cause confusion, the comma may be placed outside the quotation mark.

Example: Following the phrase "silently disrobing", an odd typographical error occurs.