You can exclude assemblies from analysis by supplying a file that list
the assemblies you want to analyze (e.g. gendarme @file.list)
However it's still possible that the assembly resolver will load them to
get more details on its (e.g. types, methods) metadata. In that case
it's possible that you'll also get the crash (depending where the bug
resides).
The best (and future proof) approach is to fill a bug report
(bugzilla.novell.com) about the crash and include the offending assembly
as an attachment (it can be a private attachment). That will make sure
Gendarme (or Cecil) is fixed.
A more immediate/hackish way would be to copy all assemblies, minus the
crashing ones, into a new directory and run gendarme on them (that won't
directly load them and it will fool the resolver not to find/load them
too).
Sebastien