Chemical Thrusters- Use hydrogen fuel to get about. The traditional thrusters of FFE and FE:2. The standard.

Ion Thrusters- Uses mercury or caesium ions as fuel. It gets good mileage, but has slow thrust rates (with one exception, a shuttle that uses its own unique ion-based thrusters). A small fusion is used to heat and expel atomspheric gases for thrust while inside atomospheres.

Fusion Thrusters- Uses any gas. It heats up the gas very quickly with the fusion engine, then expels the rapidly expanding gas for thrust.

Gravitic Thruster- Uses a fusion generator to power a gravitic engine that produces equal thrust in all directions. It produces the same thrust, no matter what ship it is fitted on. If fitted to a ship that wasn't originally equiped with it, it takes up cargo space, shuts down external thrusters, and either speeds up or slows down your ship, accordingly. Though it usually slows down small ships, many traders buy it to increase their thrust factors, either main or retro.

Thrusters cause damage. Let's face it, they don't keep people away from shuttle launches because the astronauts don't like flash photography.

Each type of thruster would have its own damage rating at various distances. Ion engines would cause radiation damage. Chemical thrusters, as well as internal fusion and fission engines, would cause large amounts of heat damage. Gravitic engines, if included, would add to hull stress and possibly hull damage if a ship got too close.
External fission or fusion engines would obviously have devastating effects for ships that venture too close.

By simulating these effects, we add realism and perhaps even a last hope for a player wily enough to exploit this system. But the players would also have to be more careful around starports because while minor damaged cause in this way is likely to be ignored, the police will recognize roasting something with your thrusters as an attack.

Hyperdrives

Background: Some time ago, the CCW (Corporate Confederation of Worlds) started a contest, with the goal of developing a hyperdrive with the capability to jump from the CCW's rim to the rim of Solnaria space in a single jump. The first organization or nation to first accomplish the goal distance was to receive a reward in their preferred currency or commodity and a very generous royalty (under the terms that the CCW would mass produce the drive). At the time, hyperdrive technology was very much in its infancy. Here are the drives:

Tyro Drive: Tyro as in 'novice' or 'beginner'. Originally simply called a hyperdrive, it was dubbed the Tyro Drive after the first contest entry, the Journeyman drive, was completed. There are 5 classes of Tyro drives.

Journeyman Drive: The Journeyman drive didn't achieve the original goal of the project, but made it apparent that the goal was within reach. There are four classes of Journeyman Drives when the game begins. Over time, four more are developed. The latest class of the Jouneyman drives had the capability to make the jump in 3.5 jumps (about a military class 1.6). Shortly after the Journeyman class 8 is unveiled, the wormhole is opened. Soon The Augur Nations are discovered.

The MasterDrive: The Augur Nations had a drive that could accomplish the goal. Once they learned of the project's existence, they immediately applied for the prize money (and got it after about a month of arguing whether they were eligible). The drive came to be known as the MasterDrive (and is roughly equivalent of a military class 4.3). Later in the game, a MasterDrive Mk 2 (military class = 5.2) is released as the hyperdrive technology of the other superpowers catches up. (It is rather important to note that aside from a few items, like the MasterDrive and wake disrupter, Augur technology is somewhat lagging behind the other nations due to the resource drought.)

Jump-Gates

Jumpgates still exist throughout much of the new galaxy. However, most nations have begun to deconstruct their old jumpgate network as hyperdrives improved over the years. The most notable exception to this rule is The Nation of Reoliscan, which has decided to see if the newer hyperdrive technology proves as reliable as the old. Furthermore, The Nation of Reoliscan doesn't perceive much of a need for hyperdrive technology, as most of the travel (of Reol) outside the Nation is done on the ships of other powers and an intricate jumpgate network already exists. Therefore, jumpgates are found connecting most important political and military systems in human space and nearly all systems in Reol space.

A more thorough explanation

Torus jump drives and Stardreams:

Everyone's still working to find a perfect combination of torus jump drives and a stardreamer-type device. Certain ships would benefit greatly from a jumpdrive, especially the tiny interplanetary craft. Perhaps a mass limit to what the jumpdrives can propel? As a famous German probably once said, "Ich weiss nicht."

Possible rules for how it works:

1) They can't work while (gravitic) distortions are near. (such as ships, planets, stations, etc.) This would allow for fair combat OR a safety circuit kicks in to prevent you from engaging/running the fastdrive near objects.

2?) The drives are shown to have a 'wake' that eventually causes major gravity problems in commonly traveled systems, throwing asteroids off course and even effecting some moons (even causing the odd starquake). The Augurs have a solution for this, a 'wake disruptor' that was invented prior to the dispersion of the galaxy.

3?) Also, maybe this drive can't propel anything more than a certain mass (only the small ships can have it, usually the ships that cannot hold a hyperdrive). This would balance the game a little bit, because ships couldn't really have both at the same time. It would also create missions for smaller ships to meet hyperdrive holding ships to transport passengers.

 
Note: Could be implemented without an overlap between ships ala Incoming's model or with a group of ships that could use both hyperdrives and fastdrives (ala Tone's suggestions).

First possibility:

Physical Explanation: The Fastdrive works by warping space-time.
From NASA's 'Warp Drive When?' web page:

Here’s the premise behind the ... "warp drive": Although Special Relativity forbids objects to move faster than light within spacetime, it is unknown how fast spacetime itself can move... In the case of the... warp drive, [a] moving section of spacetime is created by expanding spacetime behind the ship, and by contracting spacetime in front of the ship. The idea of expanding spacetime is not new. Using the "Inflationary Universe" perspective, for example, it is thought that spacetime expanded faster than the speed of light during the early moments of the Big Bang. So if spacetime can expand faster than the speed of light during the Big Bang, why not for our warp drive? These theories are too new to have either been discounted or proven viable.

Comparison Example: StarTrek, Second generation Original Elites.

Gameplay Implications: Twice as much pseudophysics and a different 'feel' than the hyperdrive. Probably too much like a warp drive for most.

Physical Explanation: The fastdrive makes a series of jumps every second which advance it a few meters each jump. This could somehow avoid the problem that causes the more traditional hyperdrive to shut down near gravity sources.

Comparison Example: I-War, Second-Generation Original Elites.

Gameplay Implications: It has a different 'feel' than the hyperdrive (one similar to the Second-Generation Original Elites), but it has the same technical specs. It involves a few more pseudo-physics, but some might not care. This seems to be the the prefered model to date, but it certainly seems like an inconsitancy unless you take a look at the psuedophysics.

Physical Explanation: As one approaches a gravity source, the hyperdrive becomes less effective as you approach the source. The fastdrive would be an enfeabled hyperdrive which gets consistently weaker as you approach a gravity well.

Comparison Example: The First-Generation Original Elites.

Gameplay Implications: It not only can be called the same as the hyperdrive, it 'feels' the same, just like the NavHS/OtherElite option. A simple, easy explanation that ties into mass-locking could be used.

Physical Explanation: NavHS.

Comparison Example: NavHS, StarTrek, the Jumpdrive of the Second-Generation Original Elites.

Gameplay Implications: Much like the third option, it has the same 'feel' all-around. Read more about it here.

Physical Explanation: Jumpgates strewn about the system, working similarly to a hyperdrive under the third option (enfeabled).

Comparison Example: An alternate universe of Babylon 5???

Gameplay Implications: Much like the third and fourth options; the same feel all around. This model could lead to more complicated navigation through systems, and also the 'clutter' of having 5-20 jumpgates strewn about the system...

Okay. We can't call it the stardreamer. I dislike the whole white noise/Zilman field explanation used. It would be far better to say there is some type of partial suspended animation. Ever read Fragments of a Hologram Rose? Something similar to the delta inducer. (and say, isn't that a good name?)