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Hello Rasheed,
Remote Buddy asks Launch Services which applications can handle a 
particular file. Launch Services itself does determine the 
applications to return based on which filetypes an application says it 
can handle. Applications do this through the Info.plist file in their 
application bundle.
Thus, if Mplayer doesn't turn up for selection, it lacks the records 
in Info.plist that would tell the rest of the system it can handle FLV 
files. You can add these records yourself, though:
1) In Finder right click on Mplayer.app and select "Show contents" 
2) Open Contents/Info.plst in a plain text editor (like Subethaedit). 
3) Search for a place that starts like
<dict> 
<key>CFBundleTypeExtensions</key> 
<array> 
<string>nut</string> 
..
and lists all the supported movie formats.
4) Add a line with 
<string>flv</string>
5) Start Mplayer. Restart Remote Buddy.
6) If it still doesn't show up in RB, use LSRefresh from this site's 
blog to manually trigger Launch Services to update its database with 
the latest information of Mplayer.app. LS doesn't always reliably 
detect changes inside bundles unless that app is copied around.
Best regards, 
Felix