MDLCT (Connection Table) Format specification
I know this is an old question but like to provide some detail since this does not seem to be documented officially anywhere.
The MDL connection table format used in MOL files is described in the CT File Formats document referenced in the first answer. This is simple ASCII text with hard linebreaks (LF or CR+LF, depending on platform). 

But there is also a special clipboard format MDL_CT created by ISIS/Draw, Accelrys/Draw etc. on Windows. This is not simply a MOL file put as text onto the clipboard. Instead each line of the molfile data is prefixed by a byte holding the number of characters, followed by the ASCII (one byte) characters of the line. The lines are not terminated by line breaks! This is basically the good old TurboPascal string format.

In addition to a single molecule the MDL_CT clipboard format also supports reactions. In that case the data comes from a RXN file, which is converted to the clipboard format the same way a molfile is: prefix each line with a length byte, remove hard linebreaks.