Open the file ~\CMSDesk\Content\ContentTree.ascx.cs and alter the following line (in the 4.0 version it can be found around line 230 within the object public TreeSiteMapProvider MapProvider):
mMapProvider.OrderBy = "NodeOrder ASC, NodeName ASC, NodeAlias ASC";
If you want to invert the order of nodes the mentioned line should look the following way:
mMapProvider.OrderBy = "NodeOrder DESC, NodeName DESC, NodeAlias DESC";