Had the same problem when i was first deciding on which to get. Went through alot of reviews and spent hours researching. So was thinking why not share these research with you.
D90:
1) Better noise reduction, allowing you to pump up to higher ISOs
2) Two dials, allowing you to adjust shutter speed and aperture at the same time in M mode
3) Lower megapixel
4) More realistic colours
5) Point focus allows you to select the point of interest
6) Lesser range of lens for selection
EOS 550D:
1) Higher megapixel (though a little overpowering for the 550D sensor, resulting in slightly more noise had high ISO)
2) Access to the large range of Cannon + 3rd Party lenses
3) Newer model=longer lasting 2nd hand market value
4) Richer Colours
5) Point focus will only focus on the centre
As you can see, both have their pros and cons. Went for the Nikon in the end due to my nature of phototaking (high ISOs).
Best way to decide, go down to the shop and try!!!