Bugging places that haven't responded is always uncomfortable, but there are some guidelines, at least informal ones.  In general, if there are no other indicators, three months is the rule of thumb.  It is appropriate at that time to contact the journal or press and inquire politely about your manuscript.  6-8 weeks is a normal response time, but 6 months is not at all unheard of.

• ADVICE. It is a great service to writers when places advertise their response time.  You then clearly know when to drop them a note or an email.  Most places list their own peculiarities in The International Directory of Literary Magazines and Small Presses.  Some places, however, don't list any time frame, and may take as long as a year to respond.  A little research ahead of time will at least help you know what you are getting into.