Here are all the USR's I have found/boiled down from the main printed rulebook and armada (so sorry if I miss a few options that are in the pdf, flipping through a book is so much easier than a pdf) (and no offense to horizon and your MMS eldar, i really like those a lot, but they're not official yet so I'm just pulling stuff from whats been printed so the rulebook MSM eldar)
Weapon USR's
Battery - uses the gunnery table to determine the dice rolled, and rolls against the armor of the target to hit.
Lance - uses its listed strength for the number of dice to roll, and hits on a 4+ regardless of the target's armor.
Persistent (renamed from pulsar, since I think its a better word that can be applied to all weapon types, you could have persistent lances, batteries, torpedoes, bombers, any weapon could be given it if chosen to) -these weapons persistent damage over 3 stages. The first stage you roll to hit like normal, the second stage you roll as many dice as scored a hit in the first stage, and the third stage rolls as many dice as scored a hit in the second stage.
Accurate - weapon systems with this rule will reroll any dice that did not score a hit on the first roll.
Heavy - weapon systems with this rule will cause 2 hits for every hit rolled.
Deadly at range (coulden't think of a name for this, maybe it should just be combined with heavy though, as thats how it is for the orks) - weapons with this rule do not get a left or right column shift due to range modifiers.
Bombardment - weapons with this rule will score hits on a 4+, and critical hits on a 4+, regardless of the targeted ship.
Leech - a Leadership check must be taken to switch to the Leech firing mode if available for the weapon system (or a declared reload ordinance check to specifically load leech ordinance), all hits caused by leech weapons will inflict a special critical hit, causing no damage, the leech effect causes the enemy ship to suffer -10cm to its movement, the effect does not accumulate for each hit, but each hit must be repaired before the -10cm is removed. Enemy ships are also unable to use "All Ahead Full" special orders when they are being leeched.
Phantom - weapon systems with this special rule will ignore the enemies armor, and instead on each roll of a 4, inflict 1 hit, and each roll of 5+ will inflict 2 hits.
Arc - weapons with this rule may split its firepower between its available firing arcs, and enemy ships count as 'closing' on the gunnery table.
Particle - hits inflicted by a weapon system with this rule will bypass shields if they rolled a '6' to hit.
Ship USR's
Massive - cannot use "Come to New Heading" special orders.
Improved sensors - this ship adds +1 to its leadership rating.
Improved targeting - this ship's weapon batteries gain a left column shift on the gunnery table.
Improved thrusters - this ship rolls 5d6 cm on "All Ahead Full" special orders.
Experimental Range Detectors - gains +2 leadership from enemy contacts that are on special orders.
Despaired thrusters - this ship rolls 3d6 cm on "All Ahead Full" special orders.
Accurate targeting - this ship does not suffer a right column shift for shooting over 30 cm.
Light frame - this ship suffers critical hits on a 4+.
Advanced targeting - this ship counts all targets as 'closing' on the gunnery table.
Primed thrusters - ships with this rule will automatically pass leadership tests to go on "All Ahead Full" special orders, but will roll 2d6 cm.
Advanced thrusters - ships with this rule will automatically pass leadership tests to go on "All Ahead Full" special orders, and will roll 4d6 cm.
Assault troops - ships with this rule gain +1 bonus on boarding actions.
Enforced Ram - this ship rolls (n+3)d6 on ramming attacks. n is its starting hits value.
Easy to defend - this ship gains a +1 bonus when defending against boarding actions.
Elite Assault troops - ships with this rule gain +2 bonus on boarding actions.
Strike teams - ships with this rule gain +1 on hit and run attacks. As do any assault boats and boarding torpedoes launched from this ship.
Enforced defenses - enemies making hit and run attacks against this ship suffer a -1 penalty on their roll.
Planetary Assault - Ships with this rule gain 2 assault points for every turn they spend landing troops or bombarding a planet.
Exterminator- A ship with this rule may exterminate a planet on a 3+.
Accurate Sabotage - ships with this rule may roll 2 1d6 for hit and run teleport attacks, and choose the result they want, with any other modifiers applied as normal.
Deadly Sabotage - ships with this rule may make one extra hit and run teleport attack per game, in addition to their normal teleport attack for that turn, this teleport attack rolls 2 1d6 plus any modifiers, and applies both results.
Demoralizing (mark of slaanesh) - any ship with this rule will cause enemy ships within 15cm to subtract 2 from their leadership.
Frenzied troops (mark of khorn/ ork warlord) - this ships boarding crew are particularly effective, the ship doubles its value in boarding actions.
Alien Environment (mark of nurgle) - the inside of this ship is either so strange or so unbearable to other races, that it may not be boarded.
Expert crew (mark of tzeentch) - this ship has one reroll in addition to any rerolls it may have gained through officers.
Advanced Damage Control - the ship may reroll the dice for damage control.
Alpha Strike - this ships crew gain +1 in the first round of a boarding action, however if the boarding action lasts for more than one round, they suffer a -1 modifier for each subsequent round.
Enhanced Maneuvering - this ship automatically passes leadership rolls to go on "Come to New Heading" special orders. This ship may also not use the "Burn Retros" special orders, but has no minimum distance requirement before turning.
Ruthless boarders - a ship with this rule may roll 2d6 for boarding actions and choose the highest result.
Unrecognizable weaknesses - this ship is so alien that any hit and run attacks made against it will roll 2d6 and choose the lowest result.
Advanced Turrets - this ships turrets may reroll any misses when defending against ordinance.
Skeleton crew - this ships boarding value counts as half (rounding up) the normal value.
Ordinance USR's
Stealth - ordinance with this rule is only hit by turrets on a 6
Resilient - ordinance with this rule will, instead of being removed fro play, remain on the board on a 4+. This can only be used once per turn, so a second situation which would remove the ordinance will do so.
Bomber Hybrid - ordinance with this rule may act as fighters, and as bombers. Their bombing runs will roll D3 hits.
Assault Hybrid - ordinance with this rule man act as fighters, and as assault boats.
Guided - ordinance with this rule that normally would be unable to alter course may turn 45 degrees before moving each turn. Ordinance with this rule will also not target friendly ships for attack runs. But they will be removed from play on a roll of 5-6 if they come into contact with a blast marker.
Melta - ordinance with this rule will inflict one automatic fire criticals for each hit scored, instead of normal damage.
Vortex - ordinance with this rule will automatically cause a critical hit for each hit scored.
Short burn - ordinance with this rule may move an extra 10cm per turn, but will run out of fuel and be removed from play on a d6 roll of a 6 each turn it moves.
I didnt get to everything, trying to do this all in one sitting is making me a little woozy, but this is basically what I mean by making USR's for everything, i didnt have the admech, craftworld eldar, or rogue trader fleet lists available at the time of this posting so I did not include any of their unique rules, and I kind of blanked out on the tyranids and necrons to some extent. But I'm sure you get the general idea. I also didnt add holofields or other special shield rules, but I have some ideas in mind.
