Just a couple minor suggestions
[*] After closing a session re-set the titlebar.
[*] Write session close line to logfiles
Code:
menu @Quer.MENU {
  dclick:  {
    if ($sline($QuerWindow,0) == 1) {
      whois $sline($QuerWindow,1)
    }
  }
  lbclick: {
    sline -l $QuerWindow $1
    clear $QuerWindow
    if ($sline($QuerWindow,0) == 1) {
      quer.titlebar 
      loadbuf -pi $QuerWindow $+(QuerLogs\Quer.,$sline($QuerWindow,1),.txt)
    }
  }
  Close $$1 Conversation: {
    if ($sline($QuerWindow,0) == 1) {
      clear $QuerWindow
[color:blue]      write $+(QuerLogs\Quer.,$1,.txt) Session ended: $+([,$asctime,],$lf,$lf)
      close -m $1 | ; see below
      titlebar $QuerWindow[/color]
      dline -l $QuerWindow $sline($QuerWindow,1).ln
    }
  }
  Delete $$1 History: {
    if ($sline($QuerWindow,0) == 1) {
      clear $QuerWindow
[color:blue]      close -m $1 | ; see below
      titlebar $QuerWindow[/color]
      dline -l $QuerWindow $sline($QuerWindow,1).ln
      .remove $+(QuerLogs\Quer.,$1,.txt)
    }
  }
}

And maybe the on open wasn't great to parse the message from, it doesn't differentiate between text and action. Perhaps hiding the query would be better.
Code:
on ^*:open:?:*:{ query -n $nick | window -h $nick }
on ^*:text:*:?:{ quer.open.and.text.event $1- }
on ^*:action:*:?:{ quer.open.and.text.event $1- }


But then of course you need to change the quer.open.and.text.event alias... smile
[*] Changes to allow for event differentiating.
[*] Color for action msgs.
[*] Window button highlighting.
Code:
alias quer.open.and.text.event {
  mkdir QuerLogs
  var %a = $+([,$time(HH:nn),]) $iif($event == action,* $nick,$+(<,$nick,>)) $1-
  write $+(QuerLogs\Quer.,$nick,.txt) %a
  aline -ln $QuerWindow $nick 
  if ($sline($QuerWindow,1) == $nick) { aline -pi $iif($event == action,$color(action)) $QuerWindow %a }
  window -g1 $QuerWindow
  window -h $nick
  halt[color:green]def[/color]
}