Incase anyone's interested, if I remember right this will help getting Thief 3 Deadly Shadows working on newer systems.
First you need to update to v1.1.
Then you need the t3.exe from the Thief 3 Editor, it was obviously released long ago but shouldn't be to hard to find, unfortunately the editor download is pretty big (300+MB) and you only want that one file from it to replace the one in your Thief 3 game's system folder. They were also nice enough to remove the CD checks from the editor's t3.exe so don't use any other such files or it won't work.
After that it should be working but you may still have some problems especially if trying to play in widescreen (eg 1920x). If while trying to play in widescreen and you seem to get stuck in the menus (can't click some buttons etc) a widescreen fix could help.
I suggest you get the Widescreen fix from http://www.foxular.net/asdf/t3_widescreen.exe
And the FOV patch from http://www.widescreengamingforum.com/downloads/T3FovPatch.zip
Copy them to the game's system folder where t3.exe is and launch them from there.
There is another thing that can cause problems on Windows 7, thanks to a really stupid "feature". Windows will try and access the internet to get info on the game and if it can't or is blocked by a firewall you'll notice you CPU usage go up and the game won't start, checking Task Manager you'll see it's thanks to rundll32.exe.
If this is happens you need to do the following to get the game to launch (happens with other older games on Windows 7 also, this also works for them).
Try start the game until rundll32.exe starts abusing your CPU, once it's doing this try launch the game again, in this case t3.exe and end the task rundll32.exe before the game launches, but not to soon or you'll be back to square 1, if you don't manage to end rundll32.exe before the game starts and takes over the screen the game could be really slow because rundll32.exe is still abusing your CPU, so you could try alt tabbing out to ask manager and ending rundll32.exe.
I think that's all the problems I ran into, though it was some time ago so I may have missed one.