Unfortunately, I believe (to date), Access Point cannot create folder icon similar to what we have on Windows.
Do all users have access to all different dashboards? or certain groups can only see certain dashboards?
If it's there's no real restriction, but just preference to tidy things up, it's easier to use what Ionannis suggested. Alternatively, you could rename your Dashboard apps and prefix it with the group, e.g.: (Marketing-Sales Analysis.qvw, Finance-Forecast Analysis.qvw)
Do the users use "Ajax" or "IE Plug In" mode from their internet browser (or mix - several folks use IE plugin, others using Ajax)? If they all use Ajax, again, then you could use the category that Ionannis suggested.For Ajax mode, when users re-login, it can save the last "state" they were in. So, if they choose category "Marketing", (I believe), the next time they return to Access Point, they will be inside "Marketing" category. If it's IE plugin, you always return to the "Default" or "All" category, which then you'll see 50+ dashboards.
If you use IE plugin, then you can restrict the folder permission, (similar to AD folder permission), so that only users belong to "Marketing" group, can only see contents in "Marketing" folder (simply prevent others to see the folders by default, and only grant them if they need to).