I bought a D3100 to replace my D40. The D40 was better.
YES, I know what you mean! You are comparing the last CCD sensor camera Nikon made, the D40, with one of their earlier CMOS sensor models with poor sensor performance. Yeah...I agree, the D40 was a better imager. The D40 was the end of the line for CCD...and it had a certain "something" about its files! I liked the D40 a LOT. I bought one for my wife for Christmas. The very large pixels (only 6 million) and the CCD, plus the ability to synch flash at 1/4000,etc.. made it a great little camera.
The 3100 by comparison was awful. The D40 is sort of a hidden little gem...BIG pixels, CCD sensor, CCD color...a really nice little rig!
The D40X was the last CCD sensor Nikon slr camera. 
Still have mine in working order. But, 
the D40X lost the high speed sync from the D40. And was $200 more. 
