AdiIRC

"File -> Options -> Windows -> Save and restore open servers"

This will save all open servers as autoconnect and add all open channels as autojoin channels.

For querys a quick script could be used.

I have all servers in Server List, but need to figure out how to save all Queries automatically. :D

I'll make a small script for you and post it here a little later.

here you go :)

on *:OPEN:?:*:{
  var %name = % $+ $network $+ _query
    set -s  [ %name ] $addtok( [ %name ] ,$target,32)
}

on *:CLOSE:?:{
  var %name = % $+ $network $+ _query
  set [ %name ] $remtok( [ %name ] ,$target,1,32)
}

raw 376:*:{
  openquerys
}

raw 422:*:{
  openquerys
}

alias query {
  var %name = % $+ $network $+ _query
    set [ %name ] $addtok( [ %name ] ,$1,32)
    !query $1-
}

alias -l openquerys {
  var %name = % $+ $network $+ _query , %s = 1

  while ($gettok( [ %name ] ,%s,32)) {
    if (!$query($v1)) {
    echo -s $gettok( [ %name ] ,%s,32)
      query $gettok( [ %name ] ,%s,32)
    }
    inc %s
  }
}

Thanks, I'll see if it works.
Everything in Scripts?

Yes, just press alt + r and paste the script into a blank file, then press save :)