Lah makes a very compelling argument! I suppose that the D40 is still a very nice camera, that can handle most situations. Although, I guess that it's still better to have a body that can perform well at high ISOs over a flash. Although a flash is nice (On account of the features that it's capable of, such as bounce flash), sometimes things like bounce flash won't work (Like in a museum, or an area with high ceilings) where you'll need to use high ISOs.
He also mentioned that the body is accountable for 10% of the image, and the lens is 90%. It's a VERY good point! I like to say the the photographer is 90% of the image, the lens is 8% and the body is 2%. If we take out the photographer, it says that the body is 80% and the lens is 20% and although it may be slightly different from Lah's post, it still represents the same idea. Here on Cameralabs we see MUCH too many posts asking whether the poster should purchase say "A 550D or D90". Although the body is important, the lens is more important. I rarely see a "Should I purchase the Nikkor 35mm AF-S F1.8 or 50mm AF F1.8". Too many people try much too hard to make their minds up on a body, and after they purchase it, they keep the same old kit lens on it the whole time.
Anyways, I think that I elaborated on Lah's post too much. If you DO decide to purchase a new body, once again I'd recommend the D7000 on account of the fact that it's very good at high ISOs and has a very good IQ for the price, it's new technology and you already have some Nikkor lenses. Although once again, if the Canon feels better in the hand compared to the Nikon, pull the trigger and go for it!
And to add on to help your decision, here
's Kai's video (Fron Digitalrev) comparing the 60D to the D7000. And here
it is compared to the 7D.
Also, remember that you shouldn't upgrade for the higher MP count, 6.1MP is high enough for outstanding large prints.