While E6 answers the question of available magic pretty solidly, this is more a general question.

What effects are out of line in a low magic environment? Or rather, on the continuum of magic effects, which ones are not what we would generally think of as appropriate?


(1) Evocative energy effects.
There is not much in history about these. Historical men whose archetype is wizard, such as Archimedes, are said to have harnessed technology to create these sorts of effects, and IIRC China has some similar stories, but while Merlin is extremely powerful, I'm pretty sure he never cast fireball.
These effects can be lobbed over castle walls with a bit of help, they can injure or kill outright large numbers of soldiers, and they create an interesting game mechanical effect on the battlefield. Even though they aren't supported well by history, I think these guys work just fine, both from a game balance and from a campain balance standpoint. The spells that fit this nicely are:
Fireball, Lightning Bolt, Cone of Cold.
Acid and Sonic damage are available at low levels, but it's pretty rare to see Acid Ball, or Cone of Sound. These effects aren't out of line, but could be left open for metamagic feats. Sonic damage is generally the most powerful in a low magic campaign, as sonic damage can blow open stone walls much easier (a 20 point fireball, by rules, does 10 points, then apply hardness, likely 8, to stone, and so does electricity- a 20 point sonic blast does 20 damage, as does an acid bolt), with fire a likely secondary effect, as plenty of things can melt or burn in a fireball. I normally recommend a small buff to lightning bolt (such as +2 to the save DC) to deal with the fact that the line effect is generally much weaker than the sphere effect, and even the E6 creators believe in levelling Cone of Cold down to 3.


(2) Divination effects
Most low level divination effects are historical in nature. The most powerful is likely divination, a 3rd level clerical spell. The generally more powerful (and risky) contact other plane is out of range of most low level stuff (though, such a spell would be a fine target for an expensive ritual), and the truly powerful (find the path, discern location) are essentially out of reach entirely. In E6, you will have to deal with Clairvoyance, a flavorful and cool ability that is limited by long range, and you skip narrowly out of reach of actual Scry. You have access to Nondetection, reasonable defense against most scrying magic, and scrying magic would be a pain anyway (multi caster ritual for the fourth level spell, so the bad guy should have access to it, but not often or well, and it can mostly be defeated by a 2nd level spell).
I believe that the school of divination could use a couple low level types of effects in addition, but certainly, you shouldn't have any problems here.

(3) Polymorph and transmutation
The actual spell polymorph itself is out of reach- requiring a ritual for a medium duration spell is out of line for most heroes and villains, and the hit dice limit prevents most of the abuses in any event. There are plenty of low level effects that can confuse, however- the illusion only disguise self, and the actual trasmuting alter self are both very powerful, and represent the top (instead of the bottom) of the ability for a caster to appear falsely before you. You very likely WANT this to be the case too, so I'd say that this is mostly a feature. You do have to worry a little that there's not much way to break these spells shy of dispel magic, but that mostly just makes them real spells in the first place. In our high level games, alter self won't fool a king most of the time because some jackhole should have true sight active. While it's not appropriate for any low level to dupe a kingdom, in a world where 6th level is the top, it's not out of line. Note that low level secondary spells, such as Detect Shapechanger or whatever should be a little more helpful here too. I think we are good with the E6 limits on these spells, mostly.

(4) Non-visible buffs and debuffs
I don't think there are enough valid debuffs at low level. Forgetting slow, when was the last time you cursed someone and that made a difference in combat? There are a decent number of buffs, at least. Most importantly, I think this is the area where you can come up with the most things. I would suggest buffs and debuffs be phrased in ways like: "When you strike your foe, you steal their (strength, dexterity, health)" a bit more often. The reason is that if you come up with a buff that is about the same power level as, say, blur, you have actually buffed whichever side gets to pre-cast, and if the effect of the buff or debuff only triggers while in combat, you may have mitigated that to a degree. While the PCs often have prep time on their side, the opposite can be a fast TPK, so the game shouldn't favor prep any more than it already does. In any event, these non-visible effects can be added a lot, and mostly affect combat in mathematical ways, and as such, don't disturb the reality of the game world or ask much of that.

(5) Extra movement
While haste, longstrider, and expedite are all available and worth casting, so is fly. However, fly is pretty limited- it's the short duration one, not the much longer overland flight. I think that 3rd level spells are just about perfect for this- personally, I like dimension door, and I like the power granted by teleport, but teleport shifts campaigns around more than any other spell, and even dim door is disruptive- and mostly, when designing a world with dim door in it, you end up coming up with things that make teleportation fail under certain conditions- an arms race, as it were.
I would suggest that there be a swim speed spell, and I point out that water breathing at 3rd seems a bit high. Nothing gives a burrow speed or the earth glide ability in core, but if we are running Pathfinder, something might. These abilities might change the game in undesired ways. Spider Climb remains a good spell that is hardly ever worth casting because of the action cost, and the requirement for hands-free means that in order to use it correctly, you need to either be a caster, a fighter built around throwing weapons (seriously), or have some rule that lets you put your damned bow away without dropping it 50 feet down into the lava you are climbing above.
As a note: in organized pathfinder play, I play a summoner. My summoner's Eidolon is a smoke-pony, a pretty blue pony creature with smokey hooves that coalesce into claws when in combat, but are also able to go tendril-style and grip walls. This is normally good for a cheap laugh, especially given that most eidolons are some flavor of demon or cat and are Very Serious Indeed, but giving a pony a climb speed was so very powerful in the dungeon-crawl environment that I was shocked. Simply put, climb speeds are badass, and the reason no one casts spider climb is because it costs an action and a spell cost. But in any underground or inside situation, a climb speed is a glorious thing- not as strong as flight, but surprisingly close.

(6) Illusions
Illusions are pretty good. The most powerful ones are gone, but so is true sight. Major Image (the old spectral force) is pretty much All U Need for describing whatever it is you want to describe- more powerful ones end up with Major Image + Something. You also don't have access to Hallucinatory Terrain, Rainbow Pattern, and Shadow Evocation- any or all of these could be brought to 3rd level (Pathfinder fixes Rainbow Pattern I think, so don't level him down if we are gonna play that- Pathfinder Rainbow Pattern is legit 4th level). Shadow Evocation, in particular, is an interesting confidence play whose omission I will miss. Overall, illusions will be stronger in an E6 game, and very interesting. Your permanent image, despite being a higher level spell, is essentially a major image that sticks around when you are done fucking with it, and while good in the current game, it was VERY strong early on. Note that Improved Invisibility is accessible via ritual, but as a combat buff that should be fine, and invisibility remains very strong, and pretty strong even at 3rd level.

(7) Necromancy
I think this is the most buffed school... for clerics. While high level necromancy is clearly deadly and powerful, and mid and low levels are considered shitty, think about this- animate dead, not available to wizards unless you reduce the power level, remains available for clerics, and can make a bunch of shitty 1 hit die creatures. But a bunch of shitty 1 hit die creatures are still in the game at 6th level, and having 10 HD of them around is actually powerful. For the wizard, this would be a terrible specialization- you can't create a single undead without a houserule, and you can't cause fear yet (scare works on creatures less than 6 hit dice- there is a non-core feat that will up that from <=5 to <=7, I think, but you might consider blocking that mechanic or making it baseline). Consider adding to the school, or just let it not be that great. Necromancy run amok makes for an entirely different campaign world, after all.

(8) Mind Controls
Charm Person is the best here. There's other good enchantments, but they all amount to status modifiers (hold, daze, sleep- it's like reading a list of pokemon debuffs). Protection from Whatever is nerfed in Pathfinder to not simply eliminate these effects, and charm, straight out, so this school is in pretty great shape if we run that. The fact that the players can't access Charm Monster shouldn't really matter- for instance, you're probably doing it wrong if the evil emperor or head of the church ISN'T a humanoid in a 6th level game, so it's mostly just proof against using it on very powerful minions.
The old spell Friends still has a place in the game, because you would simply cast that and go talk to people, and they wouldn't know they were being essentially lesser charmed. I think there's plenty of design space for a spell that makes you viewed super well by everyone, but without the "oh, you tried to mentally enslave me, and it failed / ran out" aspect of charm person. In other words, I think the original author intention of charm person is, if you meet a girl, charm her, have your dirty way with her, and then the next day she isn't a fan of you anymore because the charm ran out, that's not rape. But by the plain modern interpretation of this spell, oh fuck yes it is, and of course the other implications of the spell in combat, bargaining, etc. are all modified as well. Charm Person is essentially considered an attack and it probably isn't supposed to be, and it's considered an attack because of how good it is when it lands.
In any event, there is no dominate.