A note from the shoop. I do not have any sort of collect all the X or any of that in this list as those are fairly simple and hopefully you don't need someone to tell you collecting one of every bee could be a project.
Idea (mods needed)
Build a working frame ship (RP2)
Create a deep sea oil rig like a real world one (IC2)
Find a village and then expand and rebuild it into a large 100+ population themed city (any)
Create a all in one mega factory that creates as many products as possible (any and many needed)
Take over a lich's castle and retrofit it to be your new HQ (TF)
Craft a dungeon complete with traps and invite your server friends over and ask them to beat it (any)
Create a zombified villager rehab clinic (any)
Build a world tree by hand (any)
Build a mob classic style mob spawner system (any) Bonus create a mod sorting system to go with it
Build a functional subway system with stations on your server (any but RC and SC help tons)
Build a nuclear reactor (IC2/GT) Bonus make it look like a real world one.
Create a wind farm (RP2/IC2) bonus points for style if you use Red Power windmills.
Create a canal system complete with ports and boat docks/launchers (any)
Build a player lunching system that sends the player as far as possible but lets them land safely (any)
On your server build a public post office system using your interdimensional item moving of choice (multiple mod choices for this one)
Build a HUB for your projects or for your server community (any)
Create an obstacles course have your friends try and beat each others times (any)
Recreate your favorite landmark of choice (any)
Build something overly complex to do something simple like make a shovel(as many as you can)
Build a base some place you have not done before that has its own issues. Under the sea, in the end, on a neither lake, or anyplace harsh and possibly dangerous to you. (any)
Make life hard on yourself pick a mod and then use the worst possible way use it. IE GT but use RP as your main power choice (any)
Do a Lets play. (any)
Remove your favorite mod and then try and repair the damage and get your systems working again with the missing parts redesigned using what you now have avable (any)
Killing spree... throw all your gear in a chest and grab a stone sword. See how many kills you can rack up before you die or your weapon breaks. (any)
Create a tower of Babel. Build a tower to world hight limit but each layer needs to be bigger then the one above. (any) bonus if your start from bedrock. Extra bonus if you hollow it out and build your base inside.
Minimalize yourself. Go for as long as you can stand with just what you can carry on you. You can make bags and packs and the such. Build machines and all that but you can not stay anywhere for more then 2 MC Days and then pack up what you can and your have to move. (any)
Create a Mobile base (RP2) bonus if you can make it fully featured like a stationary base.
Build a music player (any) bonus if you have selectable songs other then the MC music discs.