550 D vs 50 D Af speed, can you help me?

Researching for a potential purchase later this year or next year.....

Can anyone having experience of both tell me if there is a significant difference in AF speed/tracking accuracy between 550D and 50D?

Bird photography would be a significant use for this one, indeed the limiting factor as other uses would be less demanding. I find the 550D is cheaper, with the kit lees (no canon lenses yet), lighter, whereas 50D offers better external control, higher fps at a higher weight. 7D is not an option, too costly.

Also is there any reason apart from Megapixels to choose 60D over 50D ?

It'd cost significantly more though it'd be lighter. Eagerly await the IQ tests in the full review on this one.