When you buy a DSLR you're potentially buying into a system, and it might be worth looking at the strengths and weaknesses of that system.
Look at the ergonomics of the cameras and which one seems more intuitive to you. I personally wouldn't pay too much attention to the size / shape / weight because all the manufacturers do a range of bodies and your second one won't be the same. But things like the control layout and menu structure do persist from one body to the next. It's a personal thing. I have a Canon 350D and a Nikon D70, and I find the Canon much more intuitive; some other people would have the opposite view.
As a beginner I personally would not worry too much about the specific capabilities of any given body. They're all good these days. Again, your first DSLR is unlikely to be your last, so buying a "Brand X" camera because it has some specific feature that the equivalent "Brand Y" camera doesn't may be short-sighted. (The exception to this would be system-wide features; for example Canon and Nikon favour lens-based image stabilisation and the others favour body-based image stabilisation. That won't change any time soon.)
Look at the range of accessories and lenses available. Canon and Nikon have much broader ranges than the other manufacturers, and bigger second-hand markets. That may change over time as the other manufacturers (particularly Sony I think) gain market share, but it won't change fast. The two big manufacturers will continue to dominate the market for years yet.
Look at the capabilities of the lenses and other accessories such as flashes. Comparing Canon and Nikon (the only two I know about), I'd say that:
* they both make some stunningly good lenses and some not-so-good ones;
* Canon have a better range of telephotos;
* Canon have a better range of fast prime lenses;
* Nikon's build quality is better for 'consumer' lenses (though both have excellent build quality for 'professional' lenses);
* Nikon lenses tend to be (but aren't always) a bit more expensive than their Canon equivalents;
* Nikon's flash system is easier to control than Canon's.
And finally ... look at what your friends / family / colleagues have. It's much easier to borrow / swap bits of kit if you have compatible systems!