Despite being an ex-software developer (or perhaps that should read "software ex-developer"!), and a total geek, I've stuck with paper.
The reason? I've never found a software app that (1) feels GTD enough for me, and (2) there's a learning curve that I'm not willing to climb, at least not until I've a mind like water.
Your mileage may vary, but for flexibility, simplicity, and reliability, nothing, to me, beats paper.
Just my $0.02.