For Pathfinder, as mentioned in the comments above, Crossbow Mastery is pretty useful. Otherwise, as far as feats go, you've got 'em covered.
The Far Shot feat will turn the -2 range increment penalties into -1, which can be very useful to shoot from long range.
Here's where some cheese comes in-- when you take a 1-level dip in Rogue with the Sniper Archetype, you gain the Accuracy ability, which that further by half. This does stack RAW, which effectively doubles your range increment distance before you even see a penalty. For example, you can pick stuff off from almost half a mile away with only a -4 penalty. Granted, you'd need scrying or something to spot your targets, but your stealth check gets hilarious... Your GM will probably scowl at you for this. Pay him back by taking Leadership and Siege Engine feats... and chuck donkeys at the BBEG from the next county. On a more serious note, the Ballista is good and can be used every turn like this.
If your GM allows material from 3.5e, then you can take both Crossbow Sniper and Improved Crossbow Sniper. The former grants you half your Dex modifier to damage and a +30 feet to Sneak Attack and Skirmish ranges, and the latter bumps it up to full dex and an additional 30 feet. Furthermore, a 1-level dip in Rogue grants you a Sneak Attack, and the Craven feat from 3.5 will grant you your character level as bonus damage to SAs (at the cost of -2 will saves against fear effects).
If your GM will allow things from 3.0, you can attach a Gnome Crossbow Sight to your xbows to ignore the first two range increment penalties.
As a GM, I allow pretty much all things regarding crossbows in Pathfinder, because they're already such a sub-optimal weapon compared to bows, thanks to the absence of the strength modifier to damage and manyshot. You'll probably be using the Launching Crossbow as an Alchemist, so your experience won't be as bad as most classes, but the feat tax for using any crossbow is almost ridiculously heavy.
A little bit more cheese, but if you take a 1-level dip in Oracle, choose the Waves mystery, and take Water Sight as your first-level revelation, you'll be able to lay down Obscuring Mist a few times a day and be able to see through it without penalty. Being able to shoot with guaranteed total concealment is a huge plus to tactical fighting (its the basis for my Sniper using crossbows in my current PF game, in fact, since the concealment guarantees Sneak Attacks)
The feat Double Slice allows the attacker to add his full Strength modifier to the damage of an appropriate off-hand weapon even at range
The benefit and normal entries for the feat Double Slice say
Benefit: Add your Strength bonus to damage rolls made with your off-hand weapon.
Normal: You normally add only half of your Strength modifier to damage rolls made with a weapon wielded in your off-hand.
An appropriate off-hand weapon is either a thrown weapon or a specially built composite longbow, specially built composite shortbow, or sling:
A character gets no Strength bonus on damage rolls with a projectile weapon unless it's a specially built composite shortbow or longbow, or a sling. If the character has a penalty for low Strength, apply it to damage rolls when he uses a bow or a sling. (Buried on the Weapons page; do a search.)
Let me make it clear that the above is my reading of the feat, based on the feat's normal entry, and, really, sometimes a feat's normal entry is the worst thing about a feat. So it's possible a more generous GM may allow an attacker to add his Strength bonus to the damage dealt with his off-hand light crossbow (or pistol or bola) while receiving no Strength bonus to damage with his primary hand light crossbow, but—and I'm gonna go out on a limb here—I suspect such a GM will be in the minority.
The benefit of the feat Two-weapon Rend when used with ranged weapons will depend on the GM
The benefit of the feat Two-weapon Rend says
If you hit an opponent with both your primary hand and your off-hand weapon, you deal an additional 1d10 points of damage plus 1-1/2 times your Strength modifier. You can only deal this additional damage once each round.
So, yeah, that's actually pretty okay with a pair of thrown weapons that deal damage plus (either whole or in part) the attacker's Strength bonus like, for example, daggers or—I don't know—spears or something, but it gets a little weird when going all The Killer with a pair of hand crossbows and absurd when going all Spider-man with a pair of bolas. In any case, before you bring this to the table, ask the GM.
For example, this GM has no problem with an attacker who hits the same foe first with a primary-hand dagger then with an off-hand dagger to then deal the extra damage from the feat Two-weapon Rend just like it says. However, this GM would struggle to allow the same attacker getting 1½× his Strength bonus were the same series of attacks made with, for example, a pair of light crossbows—but as it's really difficult to maintain such a rate of fire in the typical campaign and an attacker would've devoted so many resources to doing this once per round, I might also find it difficult to say No.
These feats are unmentioned by the FAQ, and I couldn't locate any developer commentary on this. In fact, on Paizo's messageboards, this topic is rarely discussed at all (here's from 2010 and some crazy stuff from 2009). I suspect this is because both two-weapon fighters and thrown weapon warriors have better ways to spend their precious feats.
Best Answer
Properties of siege engines
Both Siege Engines and Naval Siege Engines on Proficiency say, "Siege engines are exotic weapons." Further, Siege Engines on Direct-Fire Siege Engines says that a "direct-fire weapon uses a normal attack roll," and Naval Siege Engines on Direct-Fire Siege Engines says that a "direct-fire weapon uses a normal ranged attack roll." (A gunner instead makes a targeting check to attack using an indirect-fire siege engine.) So, because a direct-fire siege engine is a ranged projectile weapon and attacks made with such a siege engine require an attack roll, any feat that mandates one or both elements (and, obviously, isn't excluded by an individual siege engine's other elements) should work normally with a direct-fire siege engine.
Keep in mind, though, that this GM would rule that a gunner does not technically wield a siege engine, but if another GM were to rule that a gunner wields a siege engine to fire it, even more feats are available.
Also, both Siege Engines and Naval Siege Engines say, "Siege engines do not gain the benefit of critical feats the crew or the crew leader may have."
Some siege engines are specifically firearms (although none mention the amount of effort—light, 1-handed, or 2-handed—necessary to employ them), so such siege engines benefit from effects that affect any, all, or generally firearms.
By contrast, a ballista "[r]esembl[es] a massive crossbow" and "is essentially a [big] heavy crossbow fixed in place" yet, technically, is not a crossbow but, instead, a ballista. A GM that nonetheless rules a ballista is just a another (albeit big) crossbow opens the door for a ballista gunner to benefit from all kinds of feats (the feat Crossbow Mastery being the most valuable).
Siege engine tips and tricks
The rules for siege engines are extremely complicated. Here're some things I happened upon that might make your life as a siege gunner easier.
Remember ammunition. A GM that rules that a ballista is just a scaled-up crossbow means a gunslinger can, for example, spend 36,800 gp on a +1 endless ammunition light ballista. While this GM wouldn't have the weapon special ability change the siege engine's Load or Aim entries, your GM may disagree. Either way, such a siege engine never wants for ammunition. Even a light ballista bolt costs 10 gp and weighs 10 lbs.
If an extremely generous GM can be persuaded (perhaps with more beer and pizza) to allow a beneficial bandolier to store ammunition for any firearm, that should include siege engines that are also firearms! This player would not expect, like, a bombard to be affected by the bandolier's reload ability as the bombard's not wielded, but a 2-lb., 1,000-gp magic item that stores three tons of standard bombard ammunition is still beautiful. A standard bombard ball, for example, costs 35 gp and weighs 30 lbs.
Make a portable, no-assembly-required siege engine. An initially mundane assembled siege engine can "be shrunk and expanded an indefinite number of times" with the spells shrink item and permanency. However, "only by the original caster" of the spell shrink item can issue such commands. Thus a gunslinger must find a way to generate the initial shrink item spell effect, maybe by making a Use Magic Device skill check to use a wand of shrink item (DC 20) or by borrowing, for example, an ioun stone (vibrant purple prism).
A strict GM may mandate the gunslinger must generate both the shrink item effect and the permanency effect, in which case the gunslinger may be better off just shoving the siege engine (ahem) whole cloth into a portable hole.
Be aware that by using siege engines you're playing a minigame that only you alone at the table might understand. Be sure the GM wants you to play that minigame before committing to it!