The major change with a raid labeled ALT RUN is that Alts and Mains are equal in priority for gear. In addition shard cost for off-set pieces and alts does not apply in such runs.

The other major difference is drops from alt runs are not eligible for enchants using raid tab mats.

FAQ (Frequently Asked Questions)
Q: My shaman is my only 80. Bob has three 80s his main is his warrior but he is running his shaman tonight. If gear drops for a Shaman I have priority right?
A: No, in an alt run all toons in that run are on equal footing with the loot council for gear.

Q: On an alt run can’t we just get rid of loot council and do /roll on everything?
A: No, Loot Council creates a fair and even distribution of loot and can be done quickly. It is a guiding principle of the guild and as such is used even in an Alt Run.

Q: I'm a Holy Pally and a Ret piece dropped. I'd like to have it, do I need to pay a shard for it?
A: No, shard cost does not apply.

Q: And I and any other pally are on equal footing with loot council for that piece even if their main spec is Ret?
A: That is correct, there is not a difference in an alt or main in an alt run.

All items D/E'd during an Alt Run will be rolled for at the end of the run.

All raids that are Alt Runs must be clearly labeled as such when they are posted.

These rules only apply to alt runs.