Both are factions in Shattrath City. The Aldor began primarily as draenei and the Scryers began primarily as blood elves competing for the favor of the Sha'tar faction of naaru. Increasing reputation with the one means that you will have less with the other. There are a few items that are different across factions, but most will be replaced with Kharazan gear - the first 10 man raid of Burning Crusade in Deadwind Pass of the Eastern Kingdoms.
The primary difference between the two (other than a few pieces of gear that can be purchased) is in their shoulder enchants.
Aldor: Tend to have more attack/spellpower and less critical strike value.
Scryers: Tend to have more critical strike value and less attack/spell power.
Both are useful to various players for various reasons.