These can be from user-made or canon campaigns. Spoilers are pretty much unavoidable, though I'll try to blank out some of the more direct stuff.
I'll start:
Her Finest HourCampaign: Blue Planet: Tenebra
This mission has some of the best and most detailed gameplay I've ever seen. Your basic task is to help win an artillery duel against the
Carthage
, but there are many ways to accomplish this and numerous secondary goals. Almost every enemy ship larger than a bomber will try to escape, but they can be stopped by disabling their engines. The final strike can result in few or many allied casualties, depending on how well you plan things.
You are able to direct the torpedo and railgun fire of two allied frigates, adding an interesting dimension to an already detailed level. This system glitches up partway through the mission, but it is still quite interesting while it lasts.
The mission ends with a choice: spare your enemy, or take vengeance on them for their past actions. The enemy Admiral is by no means evil. She cares deeply about her subordinates and belongs to a faction that is rather harsh but arguably justified. Mercy is certainly the higher decision. However, her safety is not necessarily guaranteed, if Laporte's comments are anything to go by.
One FutureCampaign: Blue Planet: Tenebra
One Future is very different from Her Finest Hour. There are few warships in the mission, the enemy leader is an evil and possibly psychotic head of a cult, and there are not many secondary objectives. Despite this, it manages to be just as entertaining.
The player pilots a powerful, heavily-modified cruiser called the Vindicator. It is armed with a heavy forward railgun and several unusual abilities, such as shielding, afterburners, and self-repair systems. They are tasked with defeating an enemy capital ship and stopping a large, inhabited asteroid from crashing into Earth.
One Future shares its basic gameplay elements with The Blade Itself, a mission from WiH's first release. However, I believe it is far superior. Piloting the Katana was a slow and indirect affair. The Vindicator feels powerful. Its main gun can be aimed by the player, and it has a great deal of agility for a warship.
One Future is innovative, unique, and fun. There are missions in Blue Planet with more emotional impact or more intricate battles, but few are as entertaining as this one.
Clash of the TitansCampaign: Freespace Port
Clash of the Titans starts out like a typical escort mission, albeit one with very high stakes. Then the Shivans throw a Demon at you.
The first attempt at this mission will almost certainly end in failure, but you are made aware of this quickly and given an opportunity to restart with a different loadout. After that, success is only moderately difficult, provided you choose a good wing configuration.
However, achieving the secondary objective and keeping the Bastion reasonably healthy is a much more difficult proposition. The Tantalus must be destroyed quickly to prevent it from launching too many strikecraft and (eventually) engaging the Bastion in a laser duel. At the same time, enough wingmen must be fighters to effectively combat the enemy bombers. The old strategy of making Alpha and Beta Ursas will not work, thanks to the FSPort's more advanced AI.
Clash of the Titans is a mission that empathizes your wingmen and tactical ability over your piloting skill, which is somewhat unusual for FS1. It is also one of the hardest and most desperate levels in the campaign. The Bastion's original goal was to engage the Lucifer in subspace, but it falls hopelessly behind and gets severely thrashed by a Shivan force with only a fraction of their flagship's power.