You can use Ninject's convention binding extensons (install it from NuGet) to do this.
Something like the following should work
kernel.Bind(x => x.FromAssembliesMatching("Apps.Web")
.SelectAllClasses()
.InheritedFrom(typeof(ICommandHandler<>))
.BindSingleInterface());
I'm not 100% sure about the FromAssembliesMatching
pattern, but you should be able to tweak that to pick up your assembly.