If I had it my way, there would be a slick gui for everything; But since we can't all have what we want: here's a handy list of commands that you can easily reference at a whim.

This list will be updated regularly!

"Physical"

How to sit: Sneak on the bottom step of any stair block and right click it. Right click again to leave.
How to trade: Sneak and right click any player to request/accept a trade. Insert your items and then click the wool on your side of the window to confirm! Easy! How to Shop: Right click a sign to buy. Left click with the requested item in hand to sell. Shops are created by placing a sign above a chest with the following format:

Line 1: LEAVE BLANK! The shop will fill this in for you.
Line 2: Quantity (Can be over 64)
Line 3: **B** Buyprice **:** Sellprice **S**
Line 4: ItemID (Use /iteminfo with the item in hand to obtain this easily)

For example, a proper sign will turn out like this:

Firewolf
16
B 15 : 5 S
Cooked Steak

Then bam! Your shop is created and protected from everything except TNT fire.
Shops can only sell one type of item at a time.
Creation requires 20 Silver and destruction refunds you 15 silver.

Teleports

/f home: Returns you to your faction home. [No Cooldown]
/home: Returns you to your last bed. You will also return here on death.[15 Minute Cooldown]
/spawn: Returns you to the city of Eldemane. [30 Minute Cooldown]
/sethome: Sets your home. Overrides your current bed. [50 Silver] /deathtp: Returns you to your last DeathChest. [100 silver]

General

/msg [player]: Sends a message to a player. Accepts partial names.
/r [message]: Reply to the last player to message you.
/mail: Manages the users mail.
/dynmap hide/show: Set your visibility on the live map.
/realname: Shows you the Minecraft.net name of a player.
/quest status: Shows you what your current objective is.
/quest abort: Cancels your current quest.

Economy

/money: Prints how much silver you currently have.
/pay [user] [amount]: Sends money to another player.
/balancetop: View the currency for everyone on the server.

Factions

/f list [page]: Show a list of the factions.
/f who [faction tag]: Show detailed information on a certain faction. Leave blank to view your own faction.
/f map [on|off]: Show an ascii-art map of the nearby territory. Per default it will render only when you use the command. If you specify on or off you will toggle if the map should render every time you enter a new chunk.
/f power [player name]: Show either your own power (if no name is specified) or another player’s power.
/f join [faction name]: Join a faction.
/f leave: Leave your faction.
/f chat [p,f,a]: Change which channel to chat in. (P: Public, F: Faction, A: Alliance)
/f home: Teleport to the faction home.

[Faction Admin/Moderator Commands]

/f create [faction tag]: Create a new faction with you as admin. [75 Silver]
/f desc [desc]: Change the faction description.
/f tag [faction tag]: Change the faction tag.
/f open: Switch if invitation is required to join. If your faction is closed invitations are required to join the faction.
/f invite [player name]: Invite a player.
/f deinvite [player name]: Remove a pending invitation.
/f sethome: Set the faction home. Must be set in owned land. [15 Silver]
/f claim: Claim the land where you are standing.
/f unclaim: Unclaim the land where you are standing.
/f owner [player name]: Set/remove ownership of claimed land.
/f ownerlist: View a list of owners for the current area. Only works inside your own faction’s territory.
/f kick [player name]: Kick a player from the faction.
/f mod [player name]: Give or revoke moderator rights to one of the members of the faction.
/f admin [player name]: Hand over your admin rights to another member.
/f title [player name] [title]: Set or remove a players title. This serves special meaning. It’s just fun and allows you to “promote” players.
/f ally [faction name]: Request/Accept an alliance with another faction.
/f neutral [faction name]: Declare neutrality with another faction.
/f enemy [faction name]: Declare another faction as an enemy.
/f money balance [faction=yours]: Show faction bank balance.
/f money deposit <amount> [faction=yours]: Deposit money into faction bank.
/f money withdraw <amount> [faction=yours]: Withdraw money from faction bank.
/f money ff <amount> <faction> <faction>: Transfer money from faction to faction.
/f money fp <amount> <faction> <player>: Transfer money from faction to player.
/f money pf <amount> <player> <faction>: Transfer money from player to faction.
(These commands are in-case someone has a faction name that is shared by a player and vice versa)

DeathTPPlus (DeathChest)

/dtplist: Lists all of your available DeathChests.
/dtpfind [#]: Prints the coords and relative direction of the specified chest. Also locks your compass to it.
/dtpreset: Resets your compass back to your spawn location.
/deathtp [#]: Teleport to your DeathChest. [100 Silver]

MyWolf

/wolfinfo [username]: Prints the information of the specified wolf. Defaults to yours if no name is specified.
/wolfskill [username]: Prints the skill progression of the players wolf. Defaults to yours if no name is specified.
/wolfname: Names your wolf.
/wolfcall: Calls your wolf to you. (Alias: /wc)
/wolfinventory: Opens your wolf's inventory. (Alias: /wi)
/wolfpickup: Toggles automatic item pickup. (Alias: /wp)
/wolfstop: Ceases your wolf's attack. (Alias: /ws)
/wolfbehavior [normal, passive, aggressive, raid]: Sets your wolf's behavior.
--Normal: Regular behavior.
--Passive: Will never attack.
--Aggressive: Attacks anything in a 10 block radius.
--Raid: Will never attack players.
/wolfrelease: Releases your wolf into the wilds. (Note: This will cause it to drop anything in its inventory!)