Here's the extended version... hope you can use the experience...
I'd have to pretty much agree with Peterson. Since purchasing my D90 I've made over 35,000 shots. Early on I used Nikon's default exposure settings regardless of the lens and found that Nikon's algorithm constantly produced over-exposed images both RAW and JPG. Although images were only 1 to 2 EV over, I found it frustrating when comparing the same subject with Canon's default algorithm. Also, I've found this same to be true with other Nikon cameras. It's much easier for me to recover data from under-exposed images than from over-exposed. Over-exposure literally obliterates data. Since then on my D90, I've gone primarily to full manual control for critical work regardless of the lens. While Nikon's algorithm, in my opinion, is probably okay for point-and-shoot (snapshots) pictures, it's simply not the optimum for critical photography. There's a huge difference between intentionally constructed photographs and snapshots. As my skills mature, I find that I become more critical of technique. Funny that I find that when I'm just shooting non-critical stuff, I still use full-auto....crazy, aye?
Regarding post processing of critical stuff, I've found that noise is virtually a non-issue when shooting at ISO under 800 althought I've noticed that there are a couple of "hot" pixels in the CMOS. They can be adjusted out using higher-end photo editing software. JPEGs are great for many images such as time-lapse work but NEF's are invaluable for critical work. I normally capture both and tease out the details at post. Digital storage management is a whole different matter.
Regardles of the situation, a camara doesn't see what our eyes/brains see. Don't be afraid to learn what works for you. Most of all --learn to enjoy your work.