Usually many that want to upgrade want a more feature rich camera. For me it was a lack of controls and features on my D40.
And now with my D90 addresses those issues. And for me it was MORE than just better sensor performance. As many strive for it but few I see actually use the 1600-3200 on a constant enough basis to give it such a high priority to base upgrade decision on. There are many other reasons that are just as important or equal weight in the decision. At least it was for me.
D90 features over D40/D60. And removed advantages that don't apply to newer cams.
1) Now AF and AF-D lenses will autofocus.
2) Bigger & Brighter viewfinder with illuminated grid.
5) Dedicated controls and buttons for Focus mode AF-S AF-C,Also button for Single-Continuous-wireless remote selection. ISO,WB,DoF buttons Metering Pattern.
6) Top LCD for seeing all settings at a glance.
7) Two thumbwheels controls for quick changing aperture and shutter.
8) dedicated button to see ISO setting in viewfinder.
9) CLS Flash commander mode for wireless controlling your flashes.
10) Auto Bracketing
11) True Battery grip with controls for vertical shots with extended battery use.
12) High ISO on the D90 is a great improvement that allows me another stop for those lower-light handheld situations. Every little bit helps.
13) Dynamic Range - The D90 gives about 1EV of additional range.
14) 3" lcd display - For these old eyes I need all the help I can get. And blurry out of focus shots I can see without zooming to delete.
15) ISO displayed in viewfinder also can change ISO on the fly with the sub-command wheel.
17) D-Lighting - Improvements there also.
18) 3D tracking - Lock on subject and during recomposing the AF Point will change to keep subject focused. Great for motion tracking?
20) Info Button - Now can get quick Top Lcd readings on back LCD with built-in changing of D-lighting,High noise NR,Picture adjustment,Function button assignment,etc.
21) Picture preview - When reviewing picture tap up once and all picture settings and exposure info displayed with small histogram all laid out in nice easy format to read.
22) Frame rate - D90 gives 50% more at 4.5fps the D40 3fps.
Many that become serious. Became frustrated with the entry level camera like the D40 within 3-9 months. I got frustrated with lack of controls and features. And those make for a more enjoyable and less frustrating experience.
.