The SkyDrive desktop app for Windows only allows synchronizing a single directory (by default C:\Users\<Username>\SkyDrive) between your hard drive and the cloud.
Using NTFS junction points you can “create a symbolic link to a directory which then functions as an alias of that directory”.
The command to execute in the SkyDrive folder is:
mklink /J <name-of-alias> <path-to-existing-folder>
(e.g. mklink /J Photos D:\Skype\Photos)
More information can be found in these articles:
Warning: Unfortunately, if you create junction points in the SkyDrive folder itself, SkyDrive will not correctly monitor for changes (see here). As a workaround you could move the original folders into the SkyDrive folder, and create junctions at the old locations to point at the same data. This way SkyDrive monitors the folders as expected.
Updates to this blog post: