Persistent Death ward can protect you from harm. Persistent spell allows the spell to last all day, and Death ward makes you immune to, among other things, negative energy.
Find a very high level paladin or archivist and get an item enchanted with "Favor of the Martyr" (spell compendium) which explicitly protects against Wrack, and all of the status effects that wrack causes.
Unfortunately, these will do nothing against the modal cleric betrayal: "I sneak into his tent, cast hold person on his helpless, sleeping form, and continue onto the rest of the camp. Then I sacrifice them all to my deity." Have a chat out of game about whether PvP is OK, and what form of PvP is a) fun, and b) right for the group.
Yes.
The phrase "including X" means that X is not a comprehensive list of effects.
The only way for Suggestion to not be stopped by Protection from Evil would be for Suggestion to not qualify as an attempt to "exercise mental control over the creature." I doubt such an interpretation exists.
For what it's worth, I believe the reference to charms, and compulsions that grant ongoing control is an intensifier clarifying that Protection from Evil will suppress spells that have already been cast on the target but are still in effect. The examples given (Charms and Compulsions) both fall into the category of long-term mental manipulation.
It is likely that at some point play testers were confused about the interaction between spells like Dominate or Charm Person and Protection From Evil, so they added an aside to address them. Asides like that aren't meant to be all-encompassing, they're simply a way of saying "yes, even these."
Appendix: English Fun Time
As with many bits of rules text, this can be interpreted several ways. The way I'm interpreting it is simply the one that strikes me as following the written text most closely, while leaving a minimum of unknowns.
There are other interpretations that are valid from an English syntax point of view, but generally leave lingering questions. Whether these interpretations are better, worse, valid, or invalid doesn't concern me here. Only whether my interpretation fits the printed text.
Okay, so let's strip down Protection From Evil to a more streamlined version that's a bit easier to talk about:
This spell blocks any attempt to exercise mental control over the target, including effects that grant the caster ongoing control over the subject. The protection suppresses the effect for the duration of the Protection From Evil effect.
I've italicized the controversial bit. The phrase "exercise mental control" isn't defined in the game, so you have to pick an interpretation. There are three reasonable ones:
An attempt to exercise control is an action that imposes a condition on a target that forces it to act in a certain way. E.g. casting the Dominate Person spell.
An attempt to exercise control is an action that gives a target a new compulsion. E.g. issuing a command via Dominate Person.
An attempt to exercise control is anything that overrides the will of a target.
You can take your pick. The first one causes the "but what's this clause for?" problem, but both of the second two line up.
For my part, I choose the third interpretation, because it feels closer to natural language, and I don't like adding rules constructs without purpose.
Let's look at an example. Say I give you a Suggestion, and order you to dig ditches until the spell ends (in 10 hours). Three hours later, the English sentence "I am exercising mental control over you" is a valid statement. Even though I'm not actively issuing new commands.
Now suppose someone casts Protection From Evil on you (and we suppose it works the way I say it does).
The English sentence "I am attempting to exercise mental control over you, but it is being suppressed by Protection From Evil" is a valid sentence, that is in agreement with the text of the spell.
Best Answer
Spend 40 or 44k on a "living figurehead" (Stormwrack) of a black, green, or copper dragon (depending on the alignment you wish to feign and the nominal mood you want it to express.) It can function once a week for 10 minutes, but gets your ship an adequate breath weapon and complete immunity to acid. Or buy a planar helm for a 2x Planar Navigation on the ship, and just take a vacation in celestia or equivalent while the storm passes (where the spell targets the ship to and from is left as an exercise for the reader.) Or spend 10k using the stronghold builder's guidebook and turn your ship into a "zone of elemental immunity."
With that said, you're epic, so epic spellcasting can trivially have a spell named "protect a ship against acid, or rather 'convert all acid in 100 miles into minty-fresh spring water' or "kill the gentleman making this acid" or "create sufficient oxidizer or base within 1000 miles to bind to floating acid and neutralize it" (call that one the snow of baking powder) "
Presuming the acid storm is indeed acidic, take a bag of holding (of maximal capacity), fill it with baking soda formed by using polymorph any object on bags of chalk dust (mineral -> mineral of same size and class will be permanent), cast energy immunity (or resistance) on yourself, fly to the heart of the storm, start dumping bags of baking soda into the storm. Use gust of wind spells to distribute it. Given the capabilities of epic parties, this process (or the reverse if the acid is a base caustic called "acid" by the natives) will sufficiently annoy the originator of the acid storms that you can have the inevitable fight with it and resolve the problem in the time honoured adventurer fashion.
However, you don't need to use epic spellcasting. Hardening (spell compendium, page 109) provides an increase in an object's hardness by 1 per every other caster level. A ship, (presuming the ship itself is non-magic), has a default hardness of wood, or 5. Presuming that you don't simply coat the ship in glass or, being epic, adamantine, that provides a 5+(21/2) hardness sufficient to deal with 15 acid damage. You can use the normal means of increasing caster level to provide a hardness that you desire.
You'll need better sails than cloth (assuming no tricks with circle magic or other caster-level increases), but again, being epic, having mithral sails is completely reasonable (or you can simply upgrade to suitably epic means of propulsion).
Depending on the nature of the acid (what kinds of substances does it react with?) you should probably polymorph-any-object the wooden planks of your ship to either adamantine, mithral, ironwood, gold, or deep crystal.)
Any kind of "real bases" , berths, or docks, that you expect to suffer from this acid-storm should be protected by permanent prismatic walls. Note that unlike other walls, prismatic walls don't have the (S) shapeable descriptor. you'll need to have the sculpt spell metamagic to make a proper conic roof. Still, it's worthwhile due to the spell/object immunity it provides.