Update: Please note the date of this post above. I compared very early versions of the two software packages at that time. Both tools have developed a lot since then and some of my statements might be quite outdated today. (For example I’m not a beginner photographer any more. )
As a beginner of photography I’m keen to find the best software package for my image processing tasks. As I wrote earlier, I shoot only in raw format for its unarguable advantages. I’ve been testing Adobe Photoshop Lightroom and Nikon Capture NX for a few weeks. By now I found a few important features of and differences between the two packages. (A more complete comparison should include Apple Aperture as well, but currently I don’t have access to any Apple computer with MacOS.)

Both software packages are targeting professional photographers and support their image processing workflow starting from raw images. Workflow support means that adjustment tools are not hidden deeply in menus and complicated toolbars but are grouped in a meaningful way and their usage is rather intuitive. It does not mean though that you can easily use all of their functionality without reading a word from their manuals (Lightroom manual and getting started guide, Capture NX manual). They are pleasant bed time readings. Both of them are available for Microsoft Windows and Apple Mac OS. Lightroom is currently US $199 while Capture NX is around US $125.

Both handles my Nikon NEF files appropriately and basic adjustments like white balance setting and exposure correction can be performed quite similarly.

Both of them promise non-destructive image editing, but fulfill this promise differently.
Capture NX keeps all the original image information in the Nikon NEF file and adds the adjustments to the file itself. You can switch on and off any of the adjustments made throughout the whole process, so the original NEF was really not destroyed. However when you would like to open the enhanced NEF file in Photoshop or just have a look at it in Picasa you cannot do that because the NEF file was changed in a secret way that is known probably only by Nikon engineers. Surely you can export your NEF file to TIFF or JPEG and continue its editing in whatever software you wish, but this is not a perfect solution. I hate closed, proprietary file formats.
Lightroom on the other hand implements non-destructivity in similar way to Picasa’s, which means not touching the source files at all but keeping the enhancement commands in a separate database. Whenever you touch an enhanced image again within or export it from Lightroom the changes stored in the database are taken into consideration. The database format is closed in this case as well, but at least the original files are still usable by others.
1 point for Lightroom.

Selective image adjustment is an interesting area of image processing. When I got involved into photography I thought that selective image adjustment – enhancing or modifying a part of a picture differently than other parts – is rather for creative designers and something that a professional photographer should avoid. Now I think that it can be useful in many cases. In Photoshop or Gimp you do such a partial enhancement mainly with layer masks. Layers are not implemented neither in Lightroom nor Capture NX.
In Capture NX you can make selective adjustments in at least two different ways. One is applying a specific enhancement only to an area selected by the Selection brush or Lasso & Marquee Tools. The other is the magic U-Point technology, that enables you to place a so called color control point on your image and modify only pixels with similar color.
In Lightroom, apart from the red eye adjustment and spot or blemish removal there is no way to do selective adjustments additionally to the red eye adjustment and spot or blemish removal there is the Targeted Adjustment tool – similar to the U-Point thing in Capture NX – to point your mouse on any area of your image and making Tone Curve or Hue/Saturation/Luminance adjustments on similar tones of the whole picture. (Thanks to Argonaut to draw my attention to this feature.) For other selective enhancements and pixel level adjustments Adobe suggests using – guess what – Adobe Photoshop.
1 point for Capture NX.

Dust or blemish removal is implemented quite differently again.
Capture NX supports the usage of dust-off reference photos taken with Nikon cameras.
In Lightroom there is a tool for for blemish removal and its affect can be copy’n'pasted – just like any other adjustment – to other images.
Different tools with similar effect. No score.

Capability of processing multiple raw formats can be an issue if you happen to use cameras from multiple vendors.
Capture NX supports only the Nikon kind of raw format, while Lightroom is marketed as something that can process more than 150. For me it’s irrelevant at this moment, so no score.

Before I discuss performance of these otherwise great software packages I must admit that it’s high time to upgrade my PC. There is an Intel Celeron 1.7 GHz CPU with 1 GB RAM in my box so the speed performance of both tools are pathetic . However Capture NX crashes systematically whenever I save a changed NEF file either as NEF or as a JPEG, but it has nothing to do with performance but rather reliability.
On the other hand when I export a file from Lightroom it performs it as a background task with supposedly lower priority and it takes ages while it’s getting completed.
No score again.

Overall, although I gave both tools 1-1 point, Adobe Photoshop Lightroom seems to be a more mature solution to me but I wouldn’t throw Nikon Capture NX out of the window yet. I’ll keep on trying and testing.