Guilds have the ability to go after a posted bounty. I imagine that this would be similar to the Wrathion's legendary questline where you take down a high ranking leader in the opposite faction in Krasarang Wilds. It's hard to solo and complete even with a small group of friends especially on an avid PvP server. In my case, we setup multiple excursions with as many guild members as possible to get this guy down in order to complete the legendary quest. This could be another way to add another element of world PvP into the game. Go after certain high value targets in the opposing faction cities and outposts. There were times where my guild was frustrated after being shut out on a progression boss and we took our anger out by invading and holding down the auction house in Orgrimmar (I believe our current record is 34 minutes, 15 seconds with a full 40 man raid group before we all eventually succumbed).
What about smaller guilds? Sometimes a larger group isn't always better. In patch 5.2, new tech is introduced where mobs will scale up or down based on the number of players involved. Perhaps a special NPC somewhere out in the world that's maybe hidden or shows up at certain times of the day? It could be visible only to the guild that has them or available to anyone.
Either way though, guild assassination missions sound like a fun activity (it'd be like going after those special faction NPCs introduced in patch 5.1).
The next challenge is to find certain locations on the map within a time limit. This might be better suited as a scavenger hunt instead. I'd say that many players already have all of Pandaria explored anyway. What could happen is that your group has a small time limit to find and gather 20 objects before the time expires. It would be a larger scale gathering mission that's impossible to do with 1 person but could be adequately completed with 10 players.
The idea behind guild challenges is that the group fly out to investigate an area only to find out that your group has waltzed into an ambush. Your job is to defend the area and secure the objectives until you break the siege or until reinforcements arrive. It boils down to a simple zone defense concept. Burning Crusade's Battle for Mount Hyjal raid is the closest thing I can think of. Your team succeeds if they can successfully defend against 6 waves.
To really make it more interesting, it could be refined to a slightly larger scale escort mission. Remember how much you thoroughly enjoyed helping Thrall escape from Durnholde Keep? Instead of one individual, your team now has to find and escort 5 different NPCs instead and ensure they get to the safe house.
There's another mission in Guild Wars 2 called the Southsun Crab Toss. The team has to bring the crab from one place to another. They cannot use any of their skills except for a special ability where they can throw their crab to another player. We can add an element from the original Lady Vashj encounter in Serpentshrine Cavern and dictate that players are unable to move if they have the crab.
This is a simple waypoint and race concept. Your job is to race from point to point before getting to across the finish line. The issue I can see is that flying mounts would trivialize much of the work (unless it's done in a style akin to the Order of the Cloud Serpent daily The Sky Race).
Don't tell me it's not popular. How many "Running of the Bulls" events involving level 1 characters have we historically seen? I remember one incident where a Blizzard blue had to step in and "discourage" people from participating due to the destabilizing effect it would have on a server.
Jumping puzzles are one of the attractions in Guild Wars 2. There's certain rewards that are obtainable by creatively jumping from position to position that just wouldn't work in World of Warcraft. The introduction of flying mounts in the game would render the challenges relatively trivial. It's possible to move challenges indoor or set them in an instanced area where there's no flying allowed. I just don't know how appealing it would be to the Warcraft playing crowd.
I haven't thought that far in advance. The current guild systems in the game don't really allow for any type of guild currency. I suppose it could be yet another way to add gold into the guild bank or even allow for guild experience to any organizations that aren't level 25 yet. Would it be suitable for another income stream of Valor or Conquest points? Maybe, but there seems to be enough methods to collect those in the game as it is. There's no guild currency or points system in place which can be used to unlock or purchase perks. For challenges like these, I'd offer up a random mix of Lesser Charms, 476 item level quality gear, and maybe some of the raiding craftable reagents (like Haunted Spirits or whatever the equivalents may be).