There's no build-in functionality to do Desktop Content Library Files defragment in Inventor, while below is some recommendation to do defragment by 3rd party tools based on the leve of defragment you want:
1. Database level defragment: (similar to the Defragment functionality in ADMS Console)
As we're using SQLite engine for Desktop Content, you can use VACUUM command to perform a database level defragment. To do this, you can either use a command-line or a GUI-based tool:
a) Command-line tool: download the command-line SQLite program from http://www.sqlite.org/download.html, extract it to the folder you store Desktop Content libraries, execute the command sqlite3.exe (e.g. sqlite3.exe "AI2010_Inventor DIN.idcl") in a command-line window with working folder set to libraries location, and type in "VACUUM;" (without the ""), wait for its finish and type ".quit" to exit the program. The whole defragment operation might take several minutes or even longer, it depends on the size of your database.
b) GUI-based tool: you can download one named SQLiteSpy from http://www.yunqa.de/delphi/doku.php/products/sqlitespy/index, open a library file with it, and type VACUUM in the query window, click "Execute SQL" to perform the operation
2. File/Disk level defragment: you can use any file/disk defragment tools like Windows build-in Disk Defragment tool, or 3rd party tool like Contig from SysInternals which is a free file-based defragment tool, or PerfectDisk, Diskeeper, etc.