Most of the people I work with use either SMAART, or MacFOH. But they aren't the cheapest out there. I think Allen and Heath may have a free RTA on their website. It's nowhere near as advanced as SMAART, but works. At least I think it's from A&H.
I don't use any RTA program right now, mainly 'cause I don't have the money to spend on all the equipment, though I do have a measurment mic for my DRPA. I'd love to pick upSMAART or MacFOH, but that's further down the road.
Upon some further investigation of my own... I stumbled across this http://www.voxengo.com/product/SPAN VST plugin that seems to do a nice job as an RTA.. and it really is Free! You need to be running some kind of audio program that supports VST plugins inorder for this to work... so it may not be ideal for everyone, but I think that you may be able to find some programs out there that are basicly a shell to alow you to use VST plugins in a stand alone manner (although I have never used any of those).
I think it's worth jumping in here and reminding people that no matter how good the RTA, you are only going to get results as good as the weakest link in the chain leading up to your software. In other words, if you are using a cheap on board laptop microphone or even just a laptop sound card, you are almost certain to get at least slightly colored results. Real professional RTA's use special microphones with very flat frequency responses and the inputs are carefully calibrated to ensure the most accurate results possible.
I realise that you're looking for a computer based solution, but here's something I've been using myself lately. I used to have a Behringer DEQ 2496 digital EQ in my rack for FOH. The outputs went south on me but the unit has a true FFT analyser built in, so I hung on to it after buying a Driverack. Behringer also sells a calibrated mic, but you can use and calibrated (flat response) condenser as long as you know the input sensitivity.
At any rate, it sits in a 1RU rack on top of the dog house of my Soundcraft now, with the mic pointed at the room. As an additional feature, I have a pair of monitor outs, one for cans and one for a wedge. I use the wedge out, through an impedance matcher into the left input and then anything I solo comes up on the analyser with the push of a button. Once I have the room set up I just switch over which inputs it's looking at and whatever I solo is displayed. Handy for tweaking monitor mixes on the fly from 150 feet away.
Anyway, they're going on eBay for around US$250 used. The calibrated mic should be about another US$30. It's a bit pricier than a software solution, but if your situation doesn't include a laptop it's worth a look.