Please take only the items you need and can use. Ask if in doubt.
Don't remove items for selling in AH, or to disenchant.
Other guildies might use them to equip.
Clear abuses of guild vault might result in demote of ranks, or even kick from guild.
Do deposit items you feel might be in use for other guildies.
Usually no grays or other junk, but some Q items might be useful for others.
Again just ask if you're in doubt.