I see from this answer that the "Your Communities" area in the top bar menu is only supposed to show the top five sites that you participate in, based on reputation. Below this are all the rest of the sites, in alphabetical order.
However, with the old top bar menu (which you can see on Area 51), the communities at the top were all the sites that you had more than 101 reputation in, even if there were more than 5, followed by the rest of the sites in alphabetical order.
I actively participate in more than 5 sites, and it would be really nice to have them all up at the top. Is there a reason why the "Your Communities" area is limited to 5 sites?
Alternatively, if you don't want to expand the "Your Communities" area (perhaps because it will push the search box down too far), could you order the "More Stack Exchange Communities" area to have all the rest of your sites on top, in order of reputation, followed by the ones you don't have accounts in?