I've been thinking about this for a few years I guess

A fairly detailed list as we go along

demographics, some sort of STEM research, security (Phoenix Under Siege)

The Tomkins File seems to be inventory type paperwork. (In another universe they have Penny Parker transform it into an accordion style folder.)

We listed some of the projects Phoenix was involved in on the Organizations page but it's very high level and definatly not complete.

We can probbaly work through the episodes started at season 2 when they introduced the foundation.

S2.E01 was Security Consultation
In the Eraser we hear about them doing surveillance for the feds and then witness location for Jimmy

Not sure what you would call the work they were doing with the kids on the wilderness trip in Final approach though.

"Community outreach"

The CompuSketch FaceFinder (yes, really) (Blow Out, Hearts of Steel)

S2 E1 The Human Factor
Acid Test Macgyver (Security Penetration Tester)

environmental research (Trail of Tears, many others), geological database including satellite images (Trail of Tears)

The Bangkok Clinic (Second Chance)

School Dropout assistance (Live and Learn)

Endangered Species Program (Black Rhino)

Don't remember the episode, but wasn't there a storyline about nuclear disarmament/deactivating nuclear armed missiles?

Early retirement - the one where Pete gets tricked into retiring.