Thanks to the very liberal hooking mechanism and no convention, plugin authors can and will put links to their option pages anywhere. I have today six different places where plugin options can be accessed from: Plugin list, Plugins menu, Appearance menu, Tools menu, Settings menu, top level. Usually they are not even ordered alphabetically. This can not be a good thing to have.
Ironically, adding a link to the plugin list is the worst documented and most tedious alternative. I think those small 'Settings' links many plugins have are the best idea and should be made the one and only standard (it keeps the menus clean!), but that might be a matter of taste.
I strongly feel that we should have one designated place where plugin settings can be accessed from. Obviously we cannot prevent authors from putting links wherever they want if we do not want to restrict the hook mechanism, but we can define a convention. And, even more important, we can create a simple method to add your link there.
Wherever we put the links, it should be as easy as that:
register_option_page(title, label, file, handler);
The backend would then automatically put the link in the correct spot. If it is easy enough, plugin authors will go with it. After a while you might even want to prevent plugins from modifying the menus at all.
Since the sidebar menu becomes confusing once many plugins are installed, an own page might be called for.