I made the switch to Canon some years back with the D60, found lots of problems and sold it and went from the Nikon D100 to the D2H. Posted all this at:
http://www.members.cox.net/d60-d100/Review.shtml
The Canon 5D has me thinking all over again, as I miss full frame, despite its harsh exposure to glass, and despite what some have said here, Canon has great glass as does Nikon. I just miss using my 105mm and 50mm as they were meant to be used, portrait photography being my favorite endeavor these days. Anyway, I'm not going to get into the digital vs film argument, too old and pretty much decided anyway if you look at the market with open eyes.
Okay, so here's the real issues:
Dust, dust dust! Neither Canon or Nikon has solved it, so don't worry. Keep a blower handy, change lenses smartly, and manage it as best you can.
Dead/Hot pixels. Okay, I have to admit this, every single Canon digital I owned (from the "G" series on down) had pixel problems, and also some firmware bugs where I had to shut down a few times for unknown reasons. The longer I owned my D60, the more pixels 'livened up'. My Nikon D100 and D2H never showed any such problems, and I still check for them. Maybe it was just my bad luck, or maybe there is an issue there, hard to say.
Digital Darkroom slave. No one says anything, but the film lab is sorely missed by digital users, and no one warns us before we make the digital plunge. Labs had VERY expensive equipment that balanced each and every print for color and density. We spend several hundred for photoshop and still have to do it manually. It sucks. Its not that digital is less accurate than film, its just that the Lab just quietly fixed the same errors on film and you never did see it. So, you save money on the lab costs, but you are stuck with the work. Fair? Hard to answer. I don't know why Kodak (who is suffering so bad financially with the collapse of film) does not market their superior software tools, SHO, GEM and ROC, tune them into an easy to use, automated post production tool (not just a PS plugin) that just does this like the Lab does and charge $49 for the package? This is the same technology used in the Labs, and Kodak owns the rights. They'd make a mint!
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Final note on switching from Canon to Nikon and vice versa (from someone who's done it and gone back). Don't listen to the voices of unreason that insist one is better than the other, its all personal preference. Both Nikon and Canon make the best cameras, and they are neck and neck, with leadership going often back and forth. Both make superior glass (superceded only by German glass, as its always been, Zeiss, Schneider, Leica) that performs well and costs about the same. In terms of the camera, Nikon tends to be designed more by an engineering standpoint with the pro photographer in mind, where Canon is more market driven. This is why Canon seems to miss the boat on certain details like mirror lock up, instant on (before the 10D), and slow focus issues (D30). Its also why their pro line is so costly, but they dare to do the full frame thing where Nikon is playing the marketing approach on the DX issue and waiting for their chance to see if full frame sells and if they can get in on a chip Fab to make it affordable. This is probably also why you get hot pixels in Canons, as they gotta sell those chips, be they good or just marginal.
I will post on my above site an article on decisions to come up shortly regarding the new crop of cameras. This is a tough one and the products are starting to get real good now. Great time for digital.