There are many types of programs for differeing applications..whats your application? Some folks can get away with just an RTA analyzer..some prefer the computer software. Some of the new DSP's (Ashly Protea, BSS Omni drives, DBX driverack etc) have their own software that is able to interface with the DSP to help you view and adjust from a laptop. Smaart is a good and common program used by many sound engineers..however while the software download is usually free--you will need to purchase a dongle interface to actually USE it, and a good flat reference mic (Earthworks M30's are nice) and a computer & cables.
Well, most companies that sell EQs that can connect to a PC will give yuo their soft with the EQ or you can download them for free from their pages. I personally use the Ashly Protea and dbx Driverack series a lot so I have their softs in my machine. Most can communicate thru serial port. As for interfacion with measurement / system adjustment purposes, SMAART has some "external equipment" libraries that allow the Eq to automatically adjust to the readings. Not always a good choice. The only really good use I've seen for this was in the kd Lang tour where the sidefills were miked, and any potential feedback that started to rise was automatically killed by SMAART.
We us two omnidrives as our house processing. Love 'em. We had a show come through last week, though, that used the SMAARTsystem and somehow had interfaced it so the eq was adjusted automatically. They left it running during the show, too--definently something I wouldn't do. Kinda different though. Definently cool for measurement though.