Update: Small and Great Wonders:
So after adding this (not yet implemented, it just took a while to gather my thoughts together), I can start polishing up the mod in terms of balance, and start to replace the placeholder graphics, and work on the governments. Afterwards, I can start to work on individual civs and unique buildings/units/etc, and finally decide whether I want aliens or not.
Small Wonders
The Mantle Complex - The Military HQ of civs is now more centralized. The Mantle Complex allows the construction of armies, and it starts auto-producing them at a slow pace (mostly for the benefit of the AI). It is required for many of the later military programs and buildings.
Fleet Logistics - Battlefield Medicine replacement. This SW will be somewhat expensive, because logistics is one of the more complex things to deal with. Requires The Mantle Complex
Advanced Tactical Academy - Stronger armies, requires a victorious army, Mantle Complex.
Letter of Marque - Spawns Q-ships at a slow pace. It is a mid-game invisible, Hidden Nationality economic raiding unit with weak combat stats, intended to attack economic units and disrupt resources without declaring war.
Galactic Confederacy Membership - This is an attempt at implementing Civ 5's World Congress into Civ 3. This small wonder doesn't do anything except produce culture, but it allows you to begin construction of the Treaty small and great wonders, which are various treaties that civs sign and are used to justify things like why you are suddenly better at killing barbarians.
Signator: Vega Convention - Reduces War Weariness. This convention establishes the Rules of War that were originally informally followed, but now codified into international law, sort of like our Geneva Convention.
Signator: Congress of Arcturus - x2 combat vs barbarians. This is similar to the Congress of Vienna and Treaty of Tordesillas, where the galaxy is divided between the major powers (real civs), at the expense of others (the barbarians).
Signator: AI Rights Bill - x2 population growth, very high maint cost. Recognizes AIs as sapient, and are considered citizens just like anyone else. Your population grows faster now, with the extra pops justified as Androids, or dedicated AI.
Signator: Rigel Bioethics Code - 1 citizen made content in all cities. Essentially this is the justification as to why you don't have highly genetically modified humans everywhere, or uplifting dogs or dolphins to become as intelligent as humans.
Naval Tradition - generates more leaders, req. Naval Tradition, victorious army
Special Economic Zone - +1 commerce per tile, 5% interest - Requires 5 Trans-Stellar Corporations
Quadrant Capital - Forbidden Palace equivalent
Tipler Oracle - Allows the Genesis Victory, +100% science - Late game SW that allows the Space Race Victory, where instead of going to Alpha Centauri, you go and build your own universe to lord over. If we're talking galaxy spanning civilizations as is, we might as well dream big.
Intelligence Agency - Same thing s regular civ
Galactic Core Science Institute - 100% science tech, req. Supermassive Black Hole resource in radius.
Matrioska Brain - 100% science, high energy cost, requires Dyson Swarm
Great Wonders
Qianliyan Telescope - 100% research speed. It is a Lagrange Telescope, but at Neptune distance, rather than Earth distance.
Space Elevator - 50% production. Goes obsolete with Gravitics.
Monte Carlo Space Station - high local happiness. Basically Las Vegas/Macau/Earth's Monte Carlo in Space.
The Heinlein Defense Grid - auto-produces defense satellites, and acts as a barracks. Since Naval Space Stations don't come until a little bit later in the game, this is useful for, if anything, a place to upgrade your units.
Crystal Ring - +2 content faces in all cities. Basically an artificial ring around whatever planet it is orbiting.
The Surya Project - +1 commerce per tile, generates a lot of culture. A massive fusion power plant, one of the first of its kind.
The Impossible Dyson - Provides free VR Infrastructure in all cities, and happiness. A simulated VR Dyson Sphere.
The Zevatron - Massive particle accelerator that produces ZeV (10^21, compared to the 10^12 that Fermilab produces) level energies.
The Grand Armada - Free Naval Space Station in all cities. Req. Victorious army.
Multivac - 100% science. Massive interlinked supercomputer.
Darwin's Zoo - Content citizens faces in all cities. Basically a super zoo containing plant and animal analogues from every settled planet in the galaxy.
The Silver River Conglomerate - Free Trans-Stellar Corporations in all cities you own
The Prometheus Shipyard - halves upgrade costs
The Argus Array - Free Lagrange Telescopes in same continent. Communication Wormhole connected telescopes, allowing a galaxy spanning telescope array.
Vulcan's Forge - Free starforges
Ringworld Culture, happy faces in all cities
Treaty: The Oort Compact - Large amounts of culture - defines sovereignty of star systems.
Treaty: Galactic Expo - some Happiness, culture - World Fair that occurs every 100 years, and later adds the Olympics to it.
Treaty: Human Heritage Congress - Large amounts of culture. The idea is that you're declaring certain things and locations to be part of the Human Heritage, as cultural icons and such.
Treaty: Galactic Trade Union - Pays for trade installations.
Treaty: Articles of Federation - Allows Diplomatic Victory. Yes, I had to include a Federation in here somehow.
EDIT: So I had to change the names of some of these slightly because of length limitations