This is the only thing I truly miss from SMF - the bookmark addon.
The biggest site I can think of that uses that type of feature and is a GREAT example of why a separate "Subscriptions" and "Bookmarks" is beneficial is Craftster.org.
When you are working on a ton of projects, it's much easier to tack off the Bookmark option on a thread and have a HUGE list of "To Do"s. Because of the sheer number of "To Do"s on a site like that, it's extremely handy to have them separated. Subscription folders are an "okay" solution, but in certain environments the other way is preferred.