Here are some guidelines by mod category/type originally written by dev_akm, modified by bben46, and made more Fallout-appropriate by yours truly.
1. Official ESM's in their correct load order
[collapsed title=Official TTW Download Instructions]
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FalloutNV.esm
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DeadMoney.esm
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HonestHearts.esm
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OldWorldBlues.esm
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LonesomeRoad.esm
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GunRunnersArsenal.esm
The Courier's Stash packs are optional.
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CaravanPack.esm
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ClassicPack.esm
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MercenaryPack.esm
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TribalPack.esm
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Fallout3.esm
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Anchorage.esm
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ThePitt.esm
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BrokenSteel.esm
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PointLookout.esm
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Zeta.esm
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TaleOfTwoWastelands.esm
text [/collapsed]
2. All other ESM files, followed by esp's in the following general order:
3. Any Unofficial patches
4. Weather/Environment/Sound mods
5. Minor mods/houses/items
6. Major Overhaul Mods (Project Nevada, EVE, Weapon Mods, Monsters)
7. Compatibility patches for said overhauls
8. Mods that conflict with above overhauls but need to take precedence (esp's like TTW_XPReduction, TTW_NoKarmaDCFollowers, T3T_TTW_ArmorTweaks, etc)
9. Grand Compatibility patches/merged leveled lists
10.Special Handling Mods that MUST override others (Deadly Reflex for Oblivion, etc)
11. Bashed patches and merged patches
12. Super Special Handling Mods that REALLY MUST override others and really be last (such as SkyRe reproccers and Automatic Variants for Skyrim)
Within that guideline, they've put certain mods (like Quest mods) towards the end if you are either working on them or haven't finished them, but then they advise to put them higher up (I would assume before the Major Overhauls) once you've completed them. I've generally always had them higher up to begin with. :)
Some Fallout weather mods like to go lower in the load order, if I remember correctly, but I really don't know if that makes much of a difference. BOSS will certainly sort those out.
I'm sure there's something I'm forgetting...edit: yeah, like SkyRe reproccers go after bashed patches, but that's fixed now