We've purchased tickets through TKTS many times and have gotten some great deals ($28/ticket for Legally Blonde, for example). Recently, we got Xanadu and 39 Steps tickets through TKTS--50% off, and the wait has never been a problem (one hour, max).
I agree with the poster who said that if you want to see a specific show, especially one that is very popular, you might do better looking at broadwaybox or simply checking at the box office of the theatre. Some shows, like Wicked and Jersey Boys, aren't available yet through TKTS because they're selling so well...
Oh, and I wanted to add, if you buy tickets at TKTS, remember to take CASH, as they don't take credit cards or checks.