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With konqueror you can copy all files (using the View->View Mode->Tree View), do paste in the directory you want and choose skip or overwrite in the dialogs that appear (they contain the size of the files).

A possible script is something like
[code:1]#!/usr/bin/env tclsh

set destination [lindex $argv 0]
set files [lrange $argv 1 [llength $argv]]

foreach file $files {
set filename [file tail $file]
set target $destination/$filename

if {[file exists $target] && [expr [file size $target] >= [file size $file]]} {
puts "skipping $file"
continue
}

puts "copying $file"
file copy -force $file $target
}[/code:1]

to use it do something like
[code:1]<scriptname> <dir> <file 1> <file 2> ... <file n>[/code:1]

Quoted

Ok, m4ktub, I'm thinking perhaps you got turned off by my example of two Mp3 collections. Or maybe you're just not a big hand holder for less than completely on-topic posts.

Neither, I had network problems. My proxy fails somethimes.

The script copies files (not directories) to a destination directory. Although it only copies files you can use it anyway like this:
[code:1]FILES="`find /home/friend1 -iname *.mp3` `find /home/friend2 -iname *.mp3`"
<scriptname> /home/MixedFriends $FILES
[/code:1]
Translation:
The shell variable FILES will hold a list of files. This list is obtained by finding all files in /home/friend1 and /home/friend2 that have a name matching *.mp3.
Then the script copies to /home/MixedFriends all the found files overwritting the smaller ones.

Hope this is clear enough about the script and command.

Now for the semi-graphical way of doing this.
In konsole write
[code:1]<scriptname> /home/MixedFriends <space>[/code:1]
In konqueror chose "Tools->Find File". Choose the directory and *.mp3 as filter; find the files; select all the results and drag them to the konsole. Then press enter and voilá :-). Easier?

Ps: About konqueror. When using tree view you can chose files from multiple hierarquies adn copy them to a single directory. Then you would have "only" to choose yes or no with duplicate files. Of couse, it can be very anoying.