How should one respond to 'Call for Paper' e-mails? Of late I have been receiving a number of e-mails with subject 'Call for Paper' and invitations to contribute to new and/or open-access publications. While most of them immediately qualify for the trash bin, some do have a professional looking layout and language. Sometimes their publisher name looks very similar to reputed publishers.

Should I create a filter to delete and mark spam for all mails with 'Call for Paper' in the subject? 

Do reputed publishers ever advertise or invite authors to contribute to their journals?
Every conference and workshop will issue a call for papers. The editors of special issues of journals may issue a call for papers. Editors of books on a special topic may have call for papers. How else will they advertise their conference, workshop, journal, book and get submission? 

Many of these will be perfectly legitimate and even highly reputable venues. Naturally, some of these might be poorly ranked conferences or even in-it-for-the-money ventures, rather than serious scientific venues. But if you mark them all as spam, how will you know what is out there to submit your papers to?

The best strategy I can think of is to create a folder to collect these call for papers and use a filter to move them into that folder. When you need to submit a paper, you can search through the folder to find an appropriate venue. As most conferences repeat yearly at roughly the same time, you can collect the names of those and the approximate due dates in another file (or calendar), so that you build a good picture of what the major events in your field are. 

Every now and again you will need to find a new forum or perhaps there will be a book that you could contribute to. By filtering all call for papers, you miss these things.

On the other hand, you can find most of this information using Google ....

Answering the title question: generally you shouldn't respond to these emails. That said, you could send an email to be asked to be removed from the mailing list, but this is probably ineffective.