I have always used Visual Studios built in GUI support for configuring my projects, often using property sheets so that several projects will use a common set.
One of my main gripes with this is managing multiple projects, configurations and platforms. If you just do everything with the main GUI (right click the project -> properties) it quickly becomes a mess, difficult to maintain and prone to bugs (like failing to correctly define some macro, or using the wrong runtime library, etc). Dealing with the fact that different people put there dependency libraries in different places (eg mine all live in "C:\Libs\[C,C++]\[lib-name]\") and then often manage the different versions of those libraries differently as well (release, debug, x86, x64, etc) is also a large problem since it vastly complicates the time to set it up on a new system, and then there is issues with version-control and keeping everyone's paths separate...
Property sheets make this a bit better, but I cant have one sheet have separate settings for different configurations and platforms (the drop down boxes a greyed out), resulting in me having many sheets which if inherited in the correct order do what I want ("x86", "x64", "debug", "release", "common", "directories" (deals with the previously mentioned dependency issue by defining user macros like BoostX86LibDir), etc) and if inherited in the wrong order (eg "common" before "x64" and "debug") lead to issues like trying to link an incorrect library version, or incorrectly naming the output...
What I want is a way of dealing with all these scattered dependencies and setting up a set of "rules" which are used by all my projects in the solution, like naming an output library as "mylib-[vc90,vc100]-[x86,x64][-d].lib", without having to do all this for each individual project, configuration and platform combination, and then keep them all correctly in sync.
I am aware of moving to entirely different systems like CMake that create the needed files, however this then complicates things elsewhere by making it so even simple tasks like adding a new file to the project then requires additional changes elsewhere, which is not something I am entirely happy with either, unless there is some with VS2010 integration which can keep track of these sorts of changes.