DBX (Harmon Professional) has Drive Racks that do Auto EQ.  This provides a GREAT! starting point.  As Jeff mentioned, nothing is better than a reference CD to get the best sound, but the Drive Racks definitely get you in the ball park
 

So does the Behringer DEQ2496 mastering processor.  It very much gets the FOH sounding very natural and flat in a room too.  Its RTA does show up the major areas of concern and corrects them well.  Fine tuning by ear (with the FOH graphic EQ) listening to the ref track after that analysis just brings it up a notch. 
 
The other modules in that mastering processor are also very handy for a live situation. Such as advanced EQ options, dynamics control, dynamically controlled EQ and feedback destroyer.  All could be handy for making a live mix sounding as best it can. 

+1 for feedback destroyer as well as the DEQ unit. I used the FBD to recreate the Bose 901 EQ curve and then tweak that to get fairly flat response to match to other monitors. mixing on Bose - bad; checking on Bose - good :-)

Te DEQ2496 is definitely worth considering. It may have the "Behringer" word attached to it but that kind of "automatic eqing" is something Behringer have been pretty good at for many years.

Like Jeff says, a 1/3 octave band graphic eq as the final thing before the amps is also pretty much essential. It can be used for some final tweaking, because even if the PA is eq'd "flat" that may not be what you want to sound like, and room acoustics change once the audience is in as well, so a straightforward "what you see is what you get" eq can be very useful for making swift corrections.

Another issue is that audience noise, especially low frequency noise, gets picked up by microphones, and stage mics with anything close enough to encourage proximity bass boost can then amplify it and create a feedback loop with the main PA and/or foldback. A graphic that shows which bands are loudest can be very useful for spotting the offending booming frequency and rolling it off a bit.

Automatic feedback killers in the foldback can be a life saver too. One thing to watch is that they do sometimes mistake a slowly swelling drone or "pure" toned held note for incipient feedback and squash it, but overall they've saved my skin many times in the days I was regularly gigging in a band with a mixture of electronic, electric and amplified acopistic instruments that played a lot of the sort of giigs - school halls, village halls and community centres etc. - where the money doesn't justify a dedicated engineer so you end up mixing everything beforehand off the stage and then have to be a musician rather than a sound engineer.

For some reason I forgot the link to the drive rack...The new version of the PA2 has PC/MAC control.
 
http://dbxpro.com/en/product_families/driverack

I have a DEQ2496 sitting here gathering dust in my rack. I used to use it for room EQ, but it was adding an unacceptable amount of hiss so it got retired.
 
Of course, a little noise wouldn't be a showstopper in a live setting. It might be worth taking out to a gig for a try. We have no out-front mixer, everything's done from the stage. Our bass player manages the PA, and while I make an effort to not butt in (for fear of inheriting that duty myself) he does need all the help he can get.
 
As usual, Jeff has good advice from his many years' experience. I would only quibble over one point: EQing the PA based on a reference recording might not yield ideal results. What sounds good for recorded music usually ends up having too much bass for live vocals.

I have heard many times a FOH PA sounding too bass heavy.  And yes the vocals get too bass heavy as a result. Everything else gets a little bass heavy.  The ref track will still reveal it.  It will have all this extra bottom end that does not need to be there.  The lower subby stuff can be pulled right back in balance with the rest of the music.  Those subs should be heard now and then for a low note.  Once you get the bottom end sorted like this the vocal sound will be more natural and less likely to boom.  The vocals in the ref CD shine and stand out effortlessly when the bottom end of the music is set under control.
 
There needs to be a controlled amount of deeper low end that needs to be let into the room.  The points where a high pass filter can be set in will start to take effect too.  Some FOH graphic EQ's have a HPF built in.  At some point when the deeper sounds are under control, the mids will start to shine through and the top end with it too.  Our ears don't have to defend against too much bottom end.  Those parts of the spectrum can be turned up a little to bring back some gain.  The ref now sounds perfect in the bottom end with no unnecessary sub things hanging under.  The subs almost disappear until a note comes along that reminds you that they are there.  A good PA can sound extraordinary under these circumstances. 
 
Getting back to the OP, at this point the mids of the reference might even sound a little forward but some slight mid range eq adjustments over a wider bandwidth with the FOH EQ can set that back into a warmer flatter sound. Remembering how the mids sound in the ref in a great studio monitoring situation is the key.