Both systems provide most anything any amateur photographer could ask for. There are a few specialty lenses that one has but the other doesn’t, but in terms of general use stuff there’s little difference. Prospective buyers are commonly advised to decide based on ergonomics and handling issues - that is, go to a camera shop and see how they feel in your hand.
You should be aware on the Nikon side that the D60 and D5000 do not have an in-body focus motor, which means that only AF-S lenses will autofocus. That’s pretty much every consumer zoom you’re likely to consider, so it’s not a terrible limitation, but if you were thinking of using your dad’s old Nikkors from the days of film it’s something to keep in mind. Also, the inexpensive Nikkor 50mm f/1.8 is not an AF-S lens. The cheap 50’s are a common way to get into indoor available light shooting, and you don’t have a ton of lens options here with the Nikons, though the recent AF-S 50 f/1.4 and new AF-S 35mm f/1.8 have mostly solved this issue.
On the Canon side, watch which kit lens you get. IIRC the XSi comes with the 18-55 IS, which is said to be optically pretty good, but previous Rebels came with an earlier non-IS version of the 18-55 which was said to be crap (not just because of the lack of IS, but just not a good lens at all).
Other than that, the cameras are pretty similar on both sides of the aisle. The entry-level stuff all has some features stripped, and not exactly the same stuff, but it’s a get one/give one sort of thing. I believe the XSi lacks a spot meter, while the D60 gets no bracketing, for example.
If you are thinking of one day purchasing more advanced gear, it’s worth noting that high-end Nikon lenses tend to be more expensive than equivalent Canons (talking about those big things you see on the sidelines of football games here). On the other hand, Canon seems far more shy about putting advanced features into their advanced amateur cameras - the Nikon D300 shares the advanced autofocus sensor of the pro-grade D3 and D3x, for example, while the Canon 50D doesn’t even approach the AF capabilities of Canon’s 1D series.
Once you’re past 5 or 6, megapixels are mostly irrelevant. 10 vs. 12 is completely irrelevant.