From reading the specs on Sony.co.uk of the HTSF1100
Sony HTSF1100
HDMI Quality Output Signal (Up to) 1080i
It would slightly defeat the purpose of having a 1080p upscalling player to connect it through the HTSF1100 to only allow 1080i.
*Edit* However from looking at the specs of the Sony TV it only appears to accept 1080i itself. So there would not be any loss if you connected the Samsung to the HTSF1100 and then from the HTSF1100 to the TV.
It also appears the HTSF1100 does not have component in sockets also.
It states it has 2 optical and 1 Coaxial digital sound connections and that it also does not accept sound through HDMI.
If this is all the case me personally I would connect the Samsung direct to the SONY40D3000 via HDMI. I would then also connect the Samsung to the HTSF1100 via a
Coaxial sound cable to get the 5.1 sound out of the HTSF1100 whilst watching a movie. (The Coaxial cable would still be needed if connecting the Samsung to the HTSF1100 via HDMI and then from the HTSF1100 to the LCD via HDMI as it appears the HTSF1100 can not handle sound through the HDMI cable).
For the xbox360 as the HTSF1100 does not appear to have component in sockets. I would connect this direct to the TV via either component or VGA cable. I personally have my 360 connected to my Panasonic LCD via VGA to free up connectors and I found the PQ to be better (Sharper) with this connector (but its really apples and oranges as others prefer Component over VGA, plus the Xbox360 Premium edition gives you the component cable free, you need to buy the VGA cable. If you have the Xbox360 core then you will need to then buy either the Component cable or the VGA to get HD images from the xbox).
I would then connect the Xbox to the HTSF1100 via an optical cable to get the 5.1 out of the xbox.
With regards to Sky. You will need to connect this to the LCD direct also via RGB scart to get the best Picture quality.
You can then connect the Red/White phono sound connectors from the Sky box to the HTSF1100 to get stereo sound from the HTSF1100 (as opposed to 5.1 which only the Optical and Coaxial will give but the normal Sky digital box does not have these connectors, Sky+ and SkyHD have an optical out to use the last free optical cable if you ever wish to upgrade).
Hope this helps
Anthony