Yes, it's gonna happen. Here's the news from ANN:
I'm pretty excited about this, but it really sucks that it will be such a long wait. I can't wait to see this.The October issue of Neo magazine (A UK Anime magazine) includes an interview with Studio Madhouse's founder, Masao Maruyama. In it he says the studio is working on a Trigun Movie that should be released in a "couple of years". The November issue of Anime Insider also confirms this news.
So come on people, feel free to express your happiness over this great news, or speculate on what in the world this movie will be about.
(Personally, I'm just happy that Masaya Onosaka will live once again as Vash. Seriously, I'm the guy's biggest fan.)