ILMerge can output .NET 2.0 or .NET 1.1 assemblies by using the /targetplatform:v1.1 switch.

At the time of writing v2.8.0626 (26th June 08) has a little problem when targeting .NET 1.1 and running on 64bit Vista.

In the log files you see this when running on x86

Set platform to 'v1.1', using directory

'C:\Windows\Microsoft.NET\Framework\v2.0.50727\..\v1.1.4322' for mscorlib.dll

But on x64

Set platform to 'v1.1', using directory

'C:\Windows\Microsoft.NET\Framework64\v2.0.50727\..\v1.1.4322'

for mscorlib.dll

But there is no such dir – .NET 1.1 is only 32bit (though obviously it runs on x64 systems) and the correct dir is

C:\Windows\Microsoft.NET\Framework\v1.1.4322

As a result you will see the following in the log file.

AssemblyResolver: Assembly 'System.Web' is referencing assembly 'System'.

AssemblyResolver: Attempting referencing assembly's directory.

AssemblyResolver: Did not find assembly in referencing assembly's directory.

AssemblyResolver: Attempting input directory.

AssemblyResolver: Did not find assembly in input directory.

AssemblyResolver: Attempting user-supplied directories.

AssemblyResolver: Did not find assembly in user-supplied directories.

....

Could not resolve type reference: [mscorlib]System.Enum.

Could not resolve type reference: [mscorlib]System.ValueType.

Could not resolve type reference: [mscorlib]System.Object.

Could not resolve type reference: [mscorlib]System.IDisposable.

....

(Missed out a few hundred lines referencing all other mscorlib etc namespaces)

ILMerge: Done.

And although it reports done and does not return an error code you will get assembly loading errors.
Workaround

Add a symlink (a sort of low level shortcut) directing ILMerge to the correct directory.

MKLINK /D C:\Windows\Microsoft.NET\Framework64\v1.1.4322

C:\Windows\Microsoft.NET\Framework\v1.1.4322