The Creation Kit wiki is a bit vague on this. Are the assoc. item "effects" stored in the CK somewhere? Are they hard-coded or can I make my own magic effects?

They're in the creation kit. Here's the wiki page on them: http://www.creationkit.com/Magic_Effect

The associated value depends on what "Effect Archetype" a spell uses.

A Light spell, for example, uses light sources as associated values. A Value or Dual Value modifier (what damage spells are) use associated values to determine which Actor Values (AVs) are boosted or lowered. Summon spells use associated values to determine what creature and / or weapon is called. Cloak effects use associated values to determine which spell the cloak "casts" on enemies in range.

Whether you can create your own item to use as an associated value depends on what type of spell you're looking at. If you're looking for a summon spell for instance, yes, you can create your own creature entry and have the new spell summon that creature for instance. You could create a new light object for a light spell.

But if you're looking at something like a Dual Value Modifier, I'm pretty sure AVs are hardcoded and you can't set your own AVs, you have to use one of the provided ones.

Excellent, that actually answers all my questions. Thanks for the great answer