Old question, but I'm surprised no one has mentioned ilmerge yet. ilmerge is from Microsoft, but not shipped with VS or the SDKs. You can download it from here though. There is also a github repository. You can also install from nuget:
PM>Install-Package ilmerge
To use:
ilmerge assembly.dll /keyfile:key.snk /out:assembly.dll /targetplatform:v4,C:\Windows\Microsoft.NET\Framework\v4.0.30319 /ndebug
If needed, You can generate your own keyfile using sn (from VS):
sn -k key.snk