I looked at this recently, and the bottom line is, there's not much in it. Both have nominal pro's and con's over each other.
So, I took a look at the phone-specific forums for the two handsets over at http://www.androidforums.com. Seems there's a lot of people complaining about known problems with lag and GPS on the Galaxy S, with a fix being promised 'soon' by Samsung. No such problems seem to be on the Desire.
As an existing Galaxy (i7500) owner, I'd be taking Samsung's idea of 'soon' with a pinch of salt, given that they've abandoned any pretence of support for my phone and left us with buggy phones and no chance of an Android update past 1.6. The Galaxy S might be nominally better than the Desire, but personally I'd be very wary of having another Samsung phone.