I use group sets to organize my groups of references, and use smart groups to pool references from related group on my desktop client (EndNote x6). The lack of smart groups in EndNote Web means that I have to check each group for a given reference instead of one combined group; the lack of group sets means that it is difficult to distinguish between groups with identical names belonging to different group sets.
For example, I have group sets named after a given set of compounds, and each group set contains a group called elastic properties that contains references pertaining to the elastic properties of that given compound class. The web client just shows me 3 groups named elastic properties. Similarly, these group sets for compound classes contain groups for individual compounds, and a smart group that combines all the references from these groups. Some of the groups contain the same references (a given reference might mention a couple of compounds), so exporting the groups individually and recombining into one file would result in duplicate references.