I've heard it both ways. Personally, I keep mine seperated. I keep my rabbits in all-wire cages in the barn with the chickens, but not right in the pen with them. The wire keeps their little feet and bellies so clean and they don't get stinky and my kids love to cuddle them and love on them. I have Holland Lops for our pets - they're just the right size for little people to hold and so sweet!
There are some illnesses that chickens and rabbits can pass to each other; it's come up in different discussion threads, but I don't know exactly what to watch out for. I know coccidia (sp?) is one - rabbits are VERY prone to it.
Guinea pigs and rabbits can co-habitate if they get along, but still not my first choice. Guinea pigs can't handle the cold, so I always put mine outside in their own all-wire cage for the spring and summer and brought them inside during the cold months. Rabbits are clean in that they won't soil their nesting space, but guinea pigs have no problem soiling every space!
Hope that helps! Rabbits and guinea pigs both make excellent pets.