My two cents' worth for the TS as a newbie...
If I were to start all over again, the most important factor I would consider is the first-party lens selection for a brand. Each camera maker has its own line-up and each offers different types of lenses for different purposes and users.
(The reason for looking at first party lenses for comparison is simply because there is better customer service support and it also ensures future camera compatibility and promises higher QC in general.)
Just to give an example, Canon has two IS lenses in the 70-200mm range: 70-200/f2.8 and 70-200/f4 both of which have good build quality and IQ. The difference is the speed and more noticeably, perhaps, the difference in price tag. For Nikon users who want to get a Nikkor 70-200 with VR, there is only one option, the 70-200/f2.8 which is comparable to the Canon in terms of performance and price, according to online reviews.
Another example is that Nikon has a 18-200mm VR lens which is very popular with people who want a one-lens solution. Canon has yet to release a similar offering.
For this reason, I would actually advise a newbie to look at Pentax because they have some really nice prime lenses in the "Limited" series. The K200 and K20 cameras seem to be highly competent offerings too.
I do think differences like this are quite subtle but they may matter to some.
But of course I shall repeat the same advice dished out by the other posters so far because it is so true. Don't decide by just looking at the brand name. Go feel the cameras for yourself, make a decision (having good friends who use the same brand helps, as you can borrow lenses from them next time) and never look back! That was how I chose my D40X to mark my foray into "serious" photography.