In Skyrim.ini Add/Edit:
[BackgroundLoad]
bBackgroundLoadLipFiles=1
bLoadBackgroundFaceGen=1
bUseMultiThreadedFaceGen=1
bBackgroundCellLoads=1
bLoadHelmetsInBackground=1
bUseMultiThreadedTrees=1
bUseBackgroundFileLoader=1
[Animation]
bMultiThreadBoneUpdate=1
[HAVOK]
iNumThreads=**
[General]
bUseThreadedTempEffects=1
bUseThreadedParticleSystem=1
In SkyrimPrefs.ini Add/Edit:
[Navmesh]
bUseThreadedMeshes=1
[Trees]
bUseMultiThreadedTrees=1
bShadowMaskZPrePass=1
[BackgroundLoad]
bBackgroundLoadLipFiles=1
bLoadBackgroundFaceGen=1
bUseMultiThreadedFaceGen=1
bBackgroundCellLoads=1
bLoadHelmetsInBackground=1
bUseMultiThreadedTrees=1
[General]
bUseThreadedParticleSystem=1
bUseThreadedBlood=1
bUseThreadedMorpher=1
bUseThreadedTempEffects=1
bUseThreadedTextures=1
bUseThreadedMeshes=1
bUseThreadedLOD=1
bUseThreadedAI=1
**For "iNumThreads" set this to the number of CPU cores your PC has. If you have 4 or more leave this as 5 (maximum).