I'd say no, even the most advanced program can not check the text for punctuation better person (familiar with all rules of punctuation, of course).
Well, if we take into account the machine, the first option, of course, will Microsoft Office Word. Word processors Word 97 and Word 7 are used to enable the checking of punctuation and style of presentation. To do this, click tools, then "Grammar." You will also be able to enable grammar checks directly in the dialog box "Options", to do this simply select the section you want.
Click "settings" and here you can ask those grammatical rules that should be validated. If there is a need to check the entire text, set the cursor at the beginning of the text and click on the "Grammar".

If you need to check only a specific segment, select a piece of text with the command "edit" "Select all" and then click "Grammar".
In addition to the word processor, the Internet you can find a lot of programs that promise to check the text for punctuation errors. Such programs have the ability to check the punctuation not only in Russian but also in many other languages.
In conclusion, we note again that while the person has failed to invent a machine that could punctuate better than the man himself. Because in the same sentence, there are several options for punctuation, it all depends on the meaning of which bears any statement, to identify this meaning only for a conscious entity.