I've got the same dilemma at the moment. My contract with Orange is up in about 9 days and I'm torn between the Desire and the Galaxy S. My brother has the Desire so I've had a good play around with that over the past few weeks, and my girlfriend has the Hero so I'm pretty clued up on HTC Android devices. These leaves the Galaxy as a bit of an unknown quantity unfortunately. I had a play around with one in the Carphone Warehouse on the weekend but there is only so much you can learn from a 5 minute session.
My main concerns with the Galaxy S are;
-No camera flash
-Build quality (plastic and light in the hand, does not feel substantial)
-Future software updates (ie, Gingerbread)
-No notification light (what a silly oversight by Samsung)
I'm definitely drifting towards the Galaxy S purely for the specifications of the device, but there are just those few remaining niggles in the back of my head. Obviously when you are making an 18/24 month commitment you don't want to have any bad feelings about it!
The SGS is not perfect, nor is any other phone, so you should probably be able to come up with some niggling points for all phones so I don't see how you could eliminate all bad feelings before a purchase.
The SGS does not have a camera flash so the Desire will be able to take pictures in darker environments than the SGS. The SGS does take better pictures though (and much better films) and even works better in evening light, despite the lack of flash, when I compared to a friend's Desire. I also took a photo of a dark room, only lit by a TV, and did the same with a Nokia N95 8GB which has an LED flash and the SGS picture was actually brighter and more visible details. So while a flash is useful it's not as big of a deal as some might think if there's differences in the camera hardware (although it's of course individual whether the actual benefits are important or not)
That the phone is light in hand is a sign of better design since it does have better hardware. Higher weight is never a good aspect of a mobile device in my view. The plastic feel is again something that you have to decide for yourself. I don't have any problems with it myself but that doesn't say how you will feel about it.
I don't think Samsung is worse than HTC on the update front. The Galaxy didn't get 2.1 due to Google's requirements but the Spica got 2.1 months before HTC Hero.
Notification LED is just something you have to live without if you get the SGS. No way around that.
But all in all you'll have to put these things against the negatives of the Desire (worse screen, very small ROM for apps, slower CPU, much slower RAM, much slower GPU, no inbuilt storage, worse audio quality etc) and decide which of the two phones match your requirements the best. In the end only you can decide what the information is worth to you.