"Secret Projects" (hereafter, simply Projects) are the Sid Meier's Alpha Centauri (SMAC) equivalent of Wonders of the World from previous Sid Meier's Civilization games. Unlike the Wonders, however, Secret Projects are never obsoleted by later tech advances.* Like other base facilities, they can only be built after the faction has discovered an associated prerequisite technology. The cost to build a Project is much more than normal base facilities of that tech level. The completion of each different Project is a unique event in the game world of Planet: once built, no other base can build another of that Project. Whereas normal base facilities affect only the base where they are built, the effects of Projects are usually faction-wide. It's a matter of good strategy to try to build and/or capture as many Projects as possible in a game. Building a Project so that your rivals can't is a perfectly valid rationale**, and each Project adds to your final score.

Several factors weigh on the decision to build a given Project. First, they're something of a luxury; at higher difficulty levels, you may not be able to complete many (or any!) Concentrate on territorial expansion, military sufficience, and building vital facilities like Recycling Tanks before starting unnecessary Projects. You can always capture them from your rivals later on. (Or can you?)

Second, while all Projects benefit your faction in some way, some are more cost-effective than others. The Projects that affect only the base where they are built are not really very good buys (e.g. Merchant Exchange, Supercollider), while the power of the Hunter-Seeker Algorithm makes it a terrific buy for its relatively meager cost.

Third, diplomatic relations with nearby factions should suggest choice of Projects; if your neighbors are hostile, hold out for military and psi-oriented Projects.

Fourth, certain Projects make more sense for particular factions than others; the Hive faction (blue, Yang) gets a Perimeter Defense at every base to simulate underground bases, so building the Citizen's Defense Force does nothing for them but keep other factions from benefitting from it. In a similar vein, the University faction (white, Zakharov) gets a free Network Node at every base; the Virtual World Project is a powerful complement to that bonus.

Fifth and finally, owning several related Projects (e.g the psi-oriented Neural Amplifier, Xenoempathy Dome, Pholus Mutagen, and Dream Twister) helps establish your faction's dominance in a particular aspect of the game, be it expansion, exploration, conquest, research, diplomacy, or economics.

"Secret Project" is kind of a funny name for them, considering you get an alert whenever a rival faction begins or completes one, and the F5 key brings up an info screen detailing where each Project was built (or is under construction).

Project                     Cost    Prerequisite Tech                       
Human Genome Project        180    (D1) Biogenetics
Weather Paradigm            180    (E1) Centauri Ecology
Merchant Exchange           180    (B1) Industrial Base
Command Nexus               180    (C2) Doctrine: Loyalty
Virtual World               270    (D2) Planetary Networks
Planetary Transit System    270    (B3) Industrial Automation
Citizen's Defense Force     270    (E3) Intellectual Integrity
Empath Guild                180    (E3) Centauri Empathy
Planetary Datalinks         270    (B4) Cyberethics
Neural Amplifier            270    (C4) Neural Grafting
Maritime Control Center     270    (E4) Doctrine: Initiative
Longevity Vaccine           270    (B5) Bio-Engineering
Supercollider               270    (D5) Applied Relativity
Xenoempathy Dome            270    (E5) Centauri Meditation
Ascetic Virtues             270    (B6) Planetary Economics
Cyborg Factory              360    (C6) Mind/Machine Interface
Hunter-Seeker Algorithm     270    (D6) Pre-Sentient Algorithms
Cloning Vats                450    (B7) Biomachinery
Theory of Everything        360    (C7) Unified Field Theory
Pholus Mutagen              400    (E7) Centauri Genetics
Living Refinery             400    (D8) Advanced Spaceflight
Universal Translator        360    (E8) Homo Superior
Nano Factory                360    (B9) Industrial Nanorobotics
Dream Twister               360    (E9) The Will to Power
Space Elevator              450    (B10) Super Tensile Solids
Network Backbone            360    (D10) Digital Sentience
Self-Aware Colony           450    (D11) Self-Aware Machines
Clinical Immortality        450    (B12) Matter Editation
Telepathic Matrix           540    (E12) Eudaimonia
Bulk Matter Transmitter     540    (B13) Matter Transmission
Singularity Inductor        540    (C15) Controlled Singularity
Voice of Planet             720    (E15) Threshold of Transcendence
Ascent to Transcendence     2000   (E15) Threshold of Transcendence

There I go, noding for numbers again. From the popularity of the other SMAC-related nodes wafting around the nodesphere, I figured the Secret Projects would be a welcome addition to the database. Actually, I was pretty surprised the Secret Projects weren't noded around the time as, say, the Alpha Centauri Tech Tree and base facilities. I've tried to provide strategic evaluation of each Project, but mostly I just find the names and animation voice-over narratives delightfully evocative.

A few people deserve thanks for input made via /msg:
* DrSeudo
** liveforever ("We have to put a man on the moon." "Why?" "To get there before the Soviets do.")