Huge spoiler there Uncle Fuzzy!!
You can also consider all the deadric sects to be factions. Such groups and others are part of the background and you see them work together. You may help them but not join them.
Be careful when you join many guilds at the same time as their rules and duties intersect.
Also: Don't let uncle grumpy ruin your fun!
Sorry man, But not once does a guild interact with another guild and it actually means something. (There is the odd occasion where you do need to interact with another guild, but nothing that will ruin a quest from either guild) You must be thinking from Morrowind when it did.
Now to answer the OP's question. There are many small guilds that have one quest related with them. Here is a list of all of them.
The Blades
Knights of the White Stallion
The Order of the Virtuous Blood
Blackwood Company (you can join for a short period of time in the Fighters guild quest)
Knights of the Thorn
Mythic Dawn (you can join for a short period of time in the Main quest)
Order of the Dragon
Enjoy, Doran