I have used both. For smallish apps, more like web pages with some functionality in them than really heavy applications that just happen to use the browser for their UI, qooxdoo is overkill. For most intranet apps I've come across, which have rich UI, several different forms, make heavy use of many different UI controls (table, tree, combos, split panes, tab views etc.) qooxdoo is IMO the better choice.
It's not that you can't build either type with one or the other. It's just that qooxdoo makes it easier to work on large code bases, provides nice but unconstraining support for a MV(C|P) architecture, has good support for various backend types (REST, RPC, with either JSON or XML) out of the box, excellent unit testing support, separation of concerns re. theming and functionality - lots of useful things, when you do a large and complex app, but not so useful and too heavy for small apps.
There's one particular weakness in barebones backbone with makes it specifically a bad choice for larger projects - its models aren't hierarchical (i.e. members in a model which are models themselves don't cascade events or JSON serialization - they are treated as plain Java objects by backbone). Qooxdoo's properties system and the built-in JSON serializer don't have this problem. OTOH, there are several backbone plugins addressing specifically this issue.
OTOH, in recent times, qooxdoo has cut out various parts to make it easy to use proper subsets of qooxdoo in smaller web apps/mobile apps, making them available separately. Therefore, learning qooxdoo and building an ecosystem around it is probably the smarter/more economical choice, for an enterprise's intranet development.
Another aspect to consider is popularity. Most web developers have not heard of qooxdoo, given that 1&1 - the backer of qooxdoo development - doesn't invest at all in marketing qooxdoo. So selling qooxdoo to your development team might prove hard, even when it's the smarter technical choice.