I don't think that there is any single 'best' methodology. As Samer indicated, the best methodology is the one that suits the needs of the situation - one of the the keys to success is belief in the solution, so any methodology that is embraced is likely appropriate for that particular environment. I have never yet found a methodology that I could implement in its entirety, rather I try and remain up to date on as many different methodologies as possible and select and adapt the appropriate elements to any given need.
In my experience, an organization is not looking for a methodology, they are looking for a bottom line benefit - shorter time to market, less rework, lower cost, etc and I find it hard to believe that the very particular needs of a specific situation can be met by a packaged methodology.
That said, they do have the advantage of allowing an organization to get up and running quickly and talking the same language, though they can quickly become limiting.