Camera shake and cropping are definite candidates, but I would say that the most likely culprit is manual focusing.
Are you using the green focus indicator light to judge focus? If not then you will almost certainly be out of focus. I find it impossible to focus by eye through my D300. Digital SLRs' focus screens are designed to show as bright an image as possible, and unlike older manual focus lenses these focus screens are much more forgiving to the image being out of focus. So, unless you have very sharp eyes, I doubt you'll be able to focus reliably just by looking at the image in the viewfinder. (FWIW I also find the LCD on the back of the camera to be insufficient to really judge focus, even at 100% zoom)
As I say, I believe, you can use the focus indicator light even with manual focus lenses (It's labelled 1 in the diagram here: http://www.dpreview.com/reviews/nikond5000/page5.asp).
If you want to check your lens, then put the camera on a tripod, focus on something stationary and bright enough to give you a good high shutter speed (say 1/500 of a second) and see what that looks like on your computer.