I have an msbuild project which builds a SLN file from visual studio which holds all the projects in (about 70+ project), and a lot of the projects are dependent on each other m
While Project Dependencies are hard to maintain and not shared across .sln files, Project References are honoured and do dictate the order consistently - see the ResolveReferences task in Microsoft.Common.targets.
ASIDE: A 'friend of mine' may 'during a refactoring' have accidentally stubbed out their Build Task and it's DependsOnTargets linkage to the Microsoft.Common.targets ResolveReferences task and ended up with ProjectReferences not being honoured in ways that sound like the question here. If you read some of the posts, you might get the idea that it's all mad shaky - it's not; the shaky bits are the Project dependencies, not the Project references.
See this excellent MSDN Blog article by Dan Moseley that really explains the topic, including some useful workaround strategies. (via this mildly related issue with building xUnit.net).