Thanks all. Update from yesterday:
nlnet Foundation: 1,184 projects
Linux Foundation: 1,000 projects
.NET Foundation: 556 projects
Eclipse: 410 projects
Free Software Foundation's GNU project: 394 packages
The Apache Foundation: 300 projects
Drupal Association: 87 projects
KDE and GNOME: a number of projects
Total: ~4000 projects.
By "foundation" I mean an umbrella organization that provides coordination, legal services, infrastructure, administration and similar services for member projects.