I have created and recently updated a mod that will allow you to share map data with people, without the problems of overwriting chunk data when simply copying region files.

The GeoSharer mod works somewhat like WorldDownloader in that it tracks all of the world data that you come across as you play on a multiplayer server. But instead of saving all of the data into a complete world save it will take a stripped down set of just the block data along with a timestamp and save it into a *.geosharer file. These *.geosharer files can then be used to rebuild world data while ensuring that only the most recent chunk data is used, which allows multiple players to share their *.geosharer files without overwriting new data with old data from another player.

To make it a bit easier to transfer files they store only the raw block data and biomes. The chunk height map, sunlight, blocklight, and entity data is all removed. Lighting is recalculated when the data is merged into a world, including stitching lighting together between chunks. Chest contents, sign text, and frame contents are not stored.

There is a companion standalone program that will merge the data into a world save. It can also create a single trimmed down *.geosharer file that discards redundant chunk data, which is useful if you have a lot of data to transfer.

To use the mod you will need forge. Drop the mod zip file into your mods directory for forge and it will automatically copy world data from any multiplayer server you are on. The *.geosharer files are saved inside your forge mods directory in the directory geosharer/, with a subdirectory of the server name you played on. There aren't any options for it at the moment sorry. Also, only overworld data is saved (this is pretty much just written for Civcraft).

To use the standalone program you will need ".NET Framework 4.0" for Windows, or Mono 2.10 or later for Mac/Linux. Extract the exe and dll files into a directory together and just run the exe - it does not need to be installed. In the program you use the file menu to pick an output directory, which for world merging is the location of the level.dat file, and to choose the *.geosharer files to input. Use the process menu to start the merging process, or to create a trimmed *.geosharer file instead. The trimmed file will go into the output directory specified, or in the current directory if one is not.

All of the source code is on GitHub: https://github.com/azirale/GeoSharer

Current binaries are there too: https://github.com/azirale/GeoSharer/tree/master/bin

Edit 2014-06-08: The UI now allows for setting an 'Up To Date' for the creation of snapshots. Any chunk data that is timestamped later than the given 'Up To Date' will not be included in a merge, allowing for earlier versions of the data to be used instead. The UI also allows for Drag Drop. Drop a single folder to set the output directory, drop any number of *.geosharer files to add them to the list of input files.