Some mods add on to vanilla, while others are total conversions that toss out vanilla in it's near entirety. If you're in the latter category, this is the thread for you, as after a few days and help from meier of pysoase, here's a list of all 53 vanilla entities that you must load to avoid crash issues.

entityName "BuffDecloakMineForMovement.entity"
entityName "BuffNeutralCapturableEntity.entity"
entityName "BuffRecentlyColonized.entity"
entityName "Debris.entity"
entityName "EmpireWindowNode.entity"
entityName "Fleet.entity"
entityName "Formation.entity"
entityName "MissionAttackPlanet.entity"
entityName "MissionBuildMines.entity"
entityName "MissionBuildStarBase.entity"
entityName "MissionCaptureResources.entity"
entityName "MissionColonize.entity"
entityName "MissionDefendFlagship.entity"
entityName "MissionExplore.entity"
entityName "MissionFosterRelationships.entity"
entityName "MissionRaid.entity"
entityName "PipCloudEnemyShips.entity"
entityName "PipCloudFriendlyShips.entity"
entityName "PipCloudModules.entity"
entityName "PipCloudPlanets.entity"
entityName "PlanetBonusSpacePony.entity"
entityName "PlanetConnection.entity"
entityName "QuestBombPlanet.entity"
entityName "QuestGiveCreditsHigh.entity"
entityName "QuestGiveCreditsLow.entity"
entityName "QuestGiveCreditsMaintain.entity"
entityName "QuestGiveCreditsMedium.entity"
entityName "QuestGiveCrystalHigh.entity"
entityName "QuestGiveCrystalLow.entity"
entityName "QuestGiveCrystalMaintain.entity"
entityName "QuestGiveCrystalMedium.entity"
entityName "QuestGiveMetalHigh.entity"
entityName "QuestGiveMetalLow.entity"
entityName "QuestGiveMetalMaintain.entity"
entityName "QuestGiveMetalMedium.entity"
entityName "QuestKillCapitalShipsHigh.entity"
entityName "QuestKillCapitalShipsMaintain.entity"
entityName "QuestKillCivilianModulesHigh.entity"
entityName "QuestKillCivilianModulesLow.entity"
entityName "QuestKillCivilianModulesMaintain.entity"
entityName "QuestKillCivilianModulesMedium.entity"
entityName "QuestKillShipsHigh.entity"
entityName "QuestKillShipsLow.entity"
entityName "QuestKillShipsMaintain.entity"
entityName "QuestKillShipsMedium.entity"
entityName "QuestKillTacticalModulesHigh.entity"
entityName "QuestKillTacticalModulesMaintain.entity"
entityName "QuestKillTacticalModulesMedium.entity"
entityName "QuestSendEnvoyLow.entity"
entityName "ResourceAsteroidCrystal.entity"
entityName "ResourceAsteroidMetal.entity"
entityName "Trigger.entity"
entityName "Weapon.entity"

I will note that I'm not entirely sure if PlanetBonusSpacePony needs to be loaded; IIRC it is tied to an achievement and gave me issues at some point. Quest entities are in a similar boat; they're all defined in Gameplay.constants but I haven't messed around with them enough to be certain that they can be removed from both entity.manifest and Gameplay.constants without issue.