AgriCraft:

• Start guide

Ars Magica 2:

• Wiki

BiblioCraft:

• Forum thread about adding books to bookcases

Botania:

• Mod website
• Feed the Beast start guide
• Really nice start guide

HarvestCraft guides:

• Wiki (link is to 'Garden' page which is the one I mostly use)

Immersive Engineering guides:

• Immersive Engineering start guide

Mariculture guides:

• Start guide

Metallurgy guides:

• Wiki
• spawn height chart
• metals effectiveness chart

MystCraft guides:

• Mystcraft Start guide (on MystCraft wiki)

Thaumcraft guides:

• Aspect Discovery Guide
• Research Helper
• Wiki

Twilight Forest guides:

• Getting started guide

Witchery guides:

• Mod website (getting started link on front page)
• Why can't I make golden chalk? (The answer is 'you need more altar power' to basically any question like this.)

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Modding guides:

• Modding with APIs