I'm not a Nikon shooter, but I would seriously doubt that a company like Adobe is left guessing at information in the NEF format as that would mean Nikon wasn't interested in professional work which we all know isn't the case! In general, the following commercial packages are going to handle the NEF format just fine:
There are more options as well, but these are amongst the most common. I've tried not to link specific versions, you should generally go with the most recent one. I couldn't do that with Capture One.
Now, some open source software also will handle the Nikon NEF format, but it is the case were there's some reverse engineering going on. Having said that, it's not so hard and it's generally been done. Bear in mind that they'll get access to a lot of images over time and Nikon is going to be pretty common. Anyways, one of the best options here is Raw Therapee which offers a host of features (and I would suggest the beta over the old, but stable version).
As for myself, I use Photoshop CS5 in general, but I've also used Raw Therapee on machines for which I don't have Photoshop installed. If you're willing to spend some money, however, I would recommend Adobe Lightroom 3 as your best choice as it's very powerful while being very friendly to the newcomer.