I love the idea of colony set up, and one day I am will definetly have one.
But I was wondering, how do you clean all the stuff (Urine, Feces, Old hay, etc etc) off the floor? Just get in there and scoop it out about once a week?

Basically, yes... but it doesn't have to be once a week. If you are feeding hay the stalks and waste (and yes, there tends to be some) cover the bunny berries and keep the rabbits quite clean. In addition, most rabbits choose a potty corner, so you can do a partial clean-out fairly often and a complete one only when needed. You can even use litter boxes, since most rabbits take quite easily to them. It is not as sanitary as raising rabbits on wire, but I've had no illness in my herd and the livers are always fine.

I have also thought about putting a litter box or somthing similar in the "Potty corner" How are popples with litter box/corner training?
Say if a rabbit had Diarrhea , How would know which one had it, if it was in a colony? Just thinking, we never had much Diarrhea, but I always want to be aware if it where to pop up
I see now how the hay would help, Hopefully I will have a colony soon!

It's good to think things through before taking the leap. If a rabbit in a colony had diarrhea, you would look for one with a stained backside. A tip-off would be a rabbit that was acting lethargic or sitting hunched up instead of hopping around or lounging comfortably. A small colony is easier to keep track of than a large one and it may be a good idea to start small and let the colony grow naturally, while keeping most of your rabbits in cages. That way you can gain some experience without putting everything at risk.

You might start with two young does, preferably sisters, who get along well and who have always lived together. They can have visits with the buck in his cage when they are old enough to breed. When they kindle, their young will take easily to colony life and you can take it from there, perhaps retaining a promising young buck as the colony stud. This should eliminate the worry of rabbits not getting along.

Very good advice!
I was thinking about Californian rabbits for a start, But I kind of want more variation in color. Like having little "Surprise colors" In the nest box. But then again, I would probably get attached to to many that way

What do you know about "Meat pen" rabbits? I have never heard of it until recently. It sound pretty interesting.

The only context I've heard the term "meat pen" is with respect to 4H showing of meat rabbit trios. I really don't know more than that... There could be another use for the term that I am not familiar with. I've never paid much attention to showing rabbits or even raising purebreds. My partner, Brian, brought home our original mutts in July 2005 ("Surprise!") and we've worked with them ever since, gradually improving our line. We do get lots of nest box surprises and have to watch that we don't get attached to any rabbit that is not clearly good breeding material.

I'm afraid I will say "Aww.. That one is so pretty. Lets keep it... and that one... and that one.." So maybe it will be best to start off the Calis. Thanks for the advice!

And then of course each person has their own preferences when it comes to what tastes good - like different types of fish I guess.

One side of our 24x12 colony went the entire first year before being cleaned out. That side had a compacted limestone floor so moisture could travel out. We put down pine pellets, shavings, and 4 bales of straw and then didn't touch it. The top 3-4" seemed quite clean, the next few inches were a bit full of rabbit droppings, and it wasn't until the last layer against the floor (anything that can absorb moisture is also going to bring up moisture keeping everything damp) that we found mold. Prefer not to do it that way again though. It turns in to more work since it took a good month to get down through all the accumulated bedding and waste to the floor and we had to be careful not to leave areas of mold uncovered.

I like the side of the colony with heavy rubber stall mats. I put down pine pellets where they are most needed and then cover in several inches of shavings. The area around the hay silo is stripped every couple weeks to remove peed on hay and that is where lots of pine pellets are placed in order to avoid them ingesting any moldy hay. The rest is stripped every 2-3 months. We are trying similar on the other side now with part done in excess stall mats and part temporarily covered in plywood for now but we used more pine pellets than the other side so we could put straw on top. Straw and hay insulate moisture leading to things remaining wetter if you don't keep something absorbent underneath or keep removing it. That side is where most of the nesting is done so they appreciate the straw while the other side is most of the food, water, a cage stack, and a pen with the occasional nest from a lower ranked doe who could not claim the more ideal territory. I'm planning to clean it out more like 3 times a year instead of once and hopefully not accumulate everything as badly.

Colony rabbits do not seem to litterbox train well. They may pick a corner to make more of a mess out of but odds are they'll pick many corners and edges making it hard to spot clean unless you are talking a small colony with only a doe or 2.

Do the rabbits every "Nibble" on the pine pellets? And if they did ingest them, would it affect the rabbits?
I really like the idea of Rubber stall mats, might have to use that or somthing similar.
Do many people keep their colonys outside, or inside, like a barn or shed?

Livestock don't really eat pine pellets. Some will grab a mouthful at first thinking it looks like feed but it does not smell like feed and it does not taste like feed so they give up. It's more a problem with the horses who will grab mouthfuls out of any open feed sack type bag they see including fertilizer and ice melt a few times. I have heard the corn cob based pellets though, while equally as absorbent and cheaper, are eaten by livestock so have mostly disappeared back off the market except small amounts in large feed stores with a lot of variety. Our local small feed store said someone's horse ate 3, 40lb bags of the stuff so they only order it by demand mostly for cattle lots.

Luckily both items just break down in to fine sawdust which does nothing except provide a ton of fiber for the digestive tract to push out. I might be worried about the horse that ate bag fulls because of impaction issues but a mouthful for a horse or a pellet here and there for a rabbit does less harm than eating pine shavings or chewing on a board.

Small indoor colonies seem more common than outdoor ones simply because of the logistics of keeping rabbits predator safe, protection from weather, and directing their digging. I have heard of a lot of people who keep the odd rabbit or 2 loose in a chicken run or coop. Just not as much breeding of outdoor colonies on the ground instead of indoors or in small fully enclosed temporary pens like tractors.