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[Puzzlemaker]

Yeah, I am playing on the second difficulty which I think is the default.  What missions can you skip without any penalties?  Is x-grog just for selling? 

[Iduno]

What missions can you skip without any penalties?

I'm trying to think of ones that penalize you for not showing up. I know there are several, but they usually tell you in the description. Even fewer if you show up, then leave right away.

X-grog is also a 2x2 healing item, but it's too big to really be good.

[Aoi]

Yeah, I am playing on the second difficulty which I think is the default.  What missions can you skip without any penalties?  Is x-grog just for selling?

There's basically only two types of missions that are 'mandatory' (as of the previous major version), and they both have prerequisites:

Spoiler (click to show/hide)

Mutant Pogroms and EuroSyndicate missions.

The former requires you to join the Mutant Alliance (which is technically not a requirement to progress in the storyline, but getting around it requires some annoying contortions), and the latter, if you rush for it, gets you mid-game weapons very early on, but they're really expensive and you'll take massive infamy penalties if you fail their missions. They're also timed, no-extraction missions that are mid-tier difficulty, so it's win-or-die for the squad.

Note that Mutant Pogroms aren't mandatory until you join the alliance, though they show up before then. If you don't mind taking the rep hit, you can pop in, try and kill a few guys, grab their loot, and bolt. There's a lot of ablative meat armorcivvies in there, so it's not too dangerous for the first few turns, and the hostiles are probably packing better gear than you at the start.

[Rince Wind]

What missions can you skip without any penalties?

I'm trying to think of ones that penalize you for not showing up. I know there are several, but they usually tell you in the description. Even fewer if you show up, then leave right away.

X-grog is also a 2x2 healing item, but it's too big to really be good.

Now that it also incurs a freshness hit it got worse, but if possible I used grog to heal my gals at the beginning because it is better than bandages. (heals more HP)
Works better once you have a bigger ship so bringing a dedicated nurse or a strong gal with it in the backback is easier.
I also enjoyed bringing the boozeosaur while I used the Thunderhorse, though more for stun removal duty in certain missions/environments.
Speaking of certain missions:

There is a third mission that incurs penalties for not showing up, but it is basically a variant of the pogrom: Mutant Suppression. It is a late game pogrom by eridians (Snakemen).

[Aoi]

What missions can you skip without any penalties?

I'm trying to think of ones that penalize you for not showing up. I know there are several, but they usually tell you in the description. Even fewer if you show up, then leave right away.

Speaking of certain missions:

There is a third mission that incurs penalties for not showing up, but it is basically a variant of the pogrom: Mutant Suppression. It is a late game pogrom by eridians (Snakemen).

...That... might be why I had problems keeping my infamy up last time I actually reached late game.

[Rince Wind]

It is a massive -2000.

[Dostoevsky]

It's also a really tough mission if you're lacking certain tech. Harsh environment and enemies that are hard to keep down (and can be fairly well armed).

First few times I had to do it I just popped in, killed a few / took some loot, bugged out. Usually lose less infamy that way and possibly get some loot.

[Robsoie]

I wonder if unfun missions like the eurosyndicate one (in which you had to kill all the well equiped enemies in a convulated town layout before a certain amount of turn without the possibility to even extract if things go badly) are more fun now that all those convulated maps have been removed and new maps have been created to replace them.

[Rince Wind]

Eurosyndikate are also entirely optional. I never saw the point.

But I havent done a mansion in my game because I don't like those.

[Chiefwaffles]

What cave missions are required to progress the Magic/Astral/Religious stuff, in that case?

That's my biggest pet peeve against X-Piratez and X-Com Files; the extremely specific requirements to get essential things and/or to get to entire chunks of content. I remember when playing X-Com Files a while ago, I didn't happen to capture any of a specific enemy that seemed to have only appeared when you did the mission to completely eliminate one of the factions. X-Com Files has an underwater arc, and you only access this entire arc if you captured the enemy that appears in only this one-time mission. Of course, there's a good chance it's changed since then. And I may have missed other opportunities, but all signs point to that being the case at the time.
X-Piratez is less of an offender, and the dependency viewing is helpful, but god it's annoying to have to actively worry about this kind of stuff.

[Iduno]

I wonder if unfun missions like the eurosyndicate one (in which you had to kill all the well equiped enemies in a convulated town layout before a certain amount of turn without the possibility to even extract if things go badly) are more fun now that all those convulated maps have been removed and new maps have been created to replace them.

Didn't Dioxine create the mansion map? I doubt the newer maps are any less annoying than the old ones, at least not intentionally.

[Aoi]

What cave missions are required to progress the Magic/Astral/Religious stuff, in that case?

Off-hand, there's a specific map that takes place in a twisty cave that branches (that's mostly one floor, thankfully) where you have to deal with The Technomancer. Who is a bastard to keep unconscious without killing her. (I ended up surrounding her with ~6 gals and repeatedly punched her in the face for 20 turns as the rest of my group finished the place.) Pretty sure it shows up as a Red Mage mission.

[Dostoevsky]

Off-hand, there's a specific map that takes place in a twisty cave that branches (that's mostly one floor, thankfully) where you have to deal with The Technomancer. Who is a bastard to keep unconscious without killing her. (I ended up surrounding her with ~6 gals and repeatedly punched her in the face for 20 turns as the rest of my group finished the place.) Pretty sure it shows up as a Red Mage mission.

I thought you weren't supposed to capture the technomancer and/or don't get anything special for a capture v. a kill? That is a mission you need to do for that chain, but capture is optional.

Spoiler (click to show/hide)

The real pain is that the technomancer mission is one of a few maps where Dioxine put a 'puzzle' that consists of a hidden enemy, forcing you to find that enemy to end the mission normally.

Anyways, I'd argue X-Piratez is so chock full of content it's okay for certain arcs to be less common / challenging.

[Aoi]

Off-hand, there's a specific map that takes place in a twisty cave that branches (that's mostly one floor, thankfully) where you have to deal with The Technomancer. Who is a bastard to keep unconscious without killing her. (I ended up surrounding her with ~6 gals and repeatedly punched her in the face for 20 turns as the rest of my group finished the place.) Pretty sure it shows up as a Red Mage mission.

I thought you weren't supposed to capture the technomancer and/or don't get anything special for a capture v. a kill? That is a mission you need to do for that chain, but capture is optional.

You don't. I just didn't check the the Technomancer page. -_-

[Puzzlemaker]

Thanks for all the advice everyone.  I was doing better, but my infamy somehow ended up at -1000?  I may have made a few mistakes.  I also learned that taking out civilian shipping will reduce your infamy as well... I just followed a ship, I didn't recognize what it was, and I landed in this weird place that had a shirtless guy that looked like a hippie.  I stopped playing, so we will see how that goes.