Walkthrough :
1. (System Targeting)
Here is my basic strategy for fighting all vessels (and it WORKS).
First, acquire the target. Scroll through the targets until you find which one you want to pummel first.
Tactically, the consensus is to eliminate smaller ships first. However, I prefer to go for the big boys and get them out of the way quickly. Your choice. My way is harder and riskier, but risk is our business, right? After aquiring the target, determine whether it is capable of cloaking. If the vessel is equipped with a cloaking device, lock your phasers onto the cloaking device immediately (hot key sequence: V and then 8). Keep in mind that the ship will probably cloak and decloak
several times, so memorize this key sequence, because you will have to re-lock each time it decloaks. If the ship is not equipped with a cloak (or you have already destroyed the
cloaking device), lock phasers onto the ship's impulse drive (hot key sequence: V and then 3). Pummel the impulse drive until the ship is immobilized (this is best accomplished by following directly behind the enemy- this approach also allows the enemy to bring the FEWEST weapons to bear on you). You can now either attack any other hostile ships or finish off the ship
you are attacking. Remember, the disabled vessel can still rotate, so stay out of its firing arcs. This is my
tried-and true tactic. Make sure you keep a close eye on the enemy if you are chasing him. If you blow out his
impulse drive, he will stop dead in his tracks, and you run the risk of colliding with him because your Starship cannot stop on a dime. So turn out of the way if you're about to crash.
One more thing: Don't lock your phasers on an enemy's disruptors or photons. All ships have more than one
phaser/disruptor, and many have multiple photon launchers. You'll spend a lot more time blowing up weaponry than
you will knocking out an impulse drive or cloak (plus, weapons are usually so small that only half your shots will actually hit it, depending on your approach angle).

2. (Use the damn hot-keys!)
The hot keys are essential for non-combat systems. If you want to
adjust your damage control in mid-battle
by using your mouse to scroll screens, you will die often. Bridge
stations should be accessed using the B key.
When you press B, your sensor display will give you a menu of all of
your bridge stations. If you want to target a
specific enemy ship component, press the V key. A similar menu will
appear. You can allocate energy or
damage control to your systems by hitting the E key, choosing a system,
and pressing the + or - keys (I find
this takes too long. Just use the Engineering Station (V2).) The
Engineering Station's Graphical interface is
much more efficient and quick to use.

3. (Damage Control)
Don't ignore your crew, but don't pay TOO much attention to them.
Robin will report every time a shield or
system is damaged. You don't need to worry when shields are hit. Worry
about damage control AFTER you are
out of harm's way. If you are under a fierce barrage, get your engines
on-line and try to get far away. If you have a single attacker, try to
finish him off (if you have a good chance), and then lick your wounds.
Mid-combat
damage control can be very fatal (unless you're allocating to life
support, warp drive, or impulse). If you're in the
middle of a fight, and all of a sudden you can't fire any weapons, this
is a tell-tale sign that you need to tear-ass
out of there and repair. Use your judgement.

4. (The Tractor-and-Plow Maneuver)
Cloaked ships getting you down? Well, if you don't want to take the
time to destroy a ship's cloaking device,
you can try this little gem. Approach a cloaking-capable ship
straight-on, firing as usual. If he tries to cloak,
lock a tractor beam on him (this works best with a Klingon B'Rel Class
Bird of Prey). Sometimes the target will
be moving too fast for a tractor lock, so it may help to damage his
impulse drive ahead of time. If you try this
enough, you may eventually lock onto him. Once that is done, you can
fire upon him mercilessly whether he is
cloaked or not. There are two things to consider here. First, if he IS
cloaked, you will do a significant amount of
damage, as his shields are not raised while cloaked. Second, and most
important, if you try this maneuver
against a larger ship (Garuda or D-7A), you can expect a LOT of
resistance. The first thing he will do is rotate
toward you and lock every weapon he has onto your tractor beam. And if
you're fighting a Garuda (or even a
Romulan Warbird), you will be in perfect range for a Plasma Torpedo
attack, which can prove quite deadly. Use
your judgement. This tactic is perfect for multiple Birds-of-Prey, but
not reliable against larger ships.

Other Tactics

Klingon D-7's and Super Cruisers

The sensors on D-7's and Super Cruisers are extended from the main part
of the ship much like the warp
nacelles of a Constitution or Excelsior. Much like a Constitution or
Excelsior you can blow the sensors off of a
D-7 making it almost as crippled as it is without impulse. Plus it just
looks cool to see a D-7 without any
sensors.

Damage Control

Reassign your damage control values to 100% for Warp and Shields, drop
Tractor Beam Repair to 0%, lock
them at those positions, this will raise all other repair levels to 75%
and allow your engineer to modify them as
needed. If the Tractor Beam is damaged and then needed later it can
usualy be repaired far more quickly than
any other system on the ship.

Your Warp drives are your life. Never allow them, through neglect, to be
destroyed. If you can't get home you fail the mission, and your crew.

Simple as that. I have never had a Tractor Beam blown off my hull mount,
I've lost my nacelles once, and believe me, I'd have traded my tractor
for them in a heartbeat!