Lemme correct some errors. 
function keydown() 
    if ( mouseon == 0 ) then 
        ActivateMouse() 
    else 
        DeactivateMouse() 
    end 
end 
  
function startup() 
    -- At startup, we'll bind the key. 
    outputChatBox( "Startup." ) 
    bindKey( "b", "down", keydown ) 
    outputChatBox( "Key binded." ) 
end 
  
addEventHandler("onClientResourceStart", getRootElement(), startup) 
  
function commands( commandName, arg, arg2 ) 
    if( arg == "keydown" ) 
        keydown() 
        outputChatBox( "key down." ) 
        return 
    elseif( arg == "mouse" ) then 
        if( arg2 == "on" ) then 
            ActivateMouse() 
            outputChatBox( "Mouse activated." ) 
        else 
            DeactivateMouse() 
            outputChatBox( "Mouse deactivated." ) 
        end 
        return 
    else 
        outputChatBox( "Bomber script is active. (c) tomozj 2008" ) 
        outputChatBox( "USAGE: /bomber [start/keydown/mouse] [on/off]" ) 
        return 
    end 
end 
  
addCommandHandler("bomber", commands, arg, arg2) 
 
All in all, you added ends before elses, which is a syntax error in Lua. Also, onClientResourceStart actually executes on resource start, (honest!) so it's redundant to have a command to execute it again. 
Oh, and I didn't check to see if it actually works, it's up to you from here.