Unfortunately you can't use If-Else-EndIf in commands....
Thank you for the quick comment, and the detailed explanation, why it isn't possible.
As someone, who also has a little xperience in programming, its quite interresting to read the details
and by the time I implemented If-Else-EndIf I had decided to limit my time on the program because I want to get it finished and move on to the next one.
..hey, no problem with that, in my opinion you have done a wonderful job, and knowing, that you put your time in another project (programW I think), which sounds very promising is perfectly ok with me (although the scripting seems to be gone, which i realy like about hkn, but the masses will kiss you for simple graphic interfaces, so its ok! ).
Btw. if you need more alpha-testers therefor, tell me...

But back to topic:

..when the only problem, why the above wouldn't work is, that the iF-Else-Endif is defined in a command, it basicly should work, if i "hard code" it in the hotkey, which only would result in a longer, more redundant hotkeydefinition, but shouldn't be a problem.
Especialy, i think i read somewhere, that you can include other hotkeyfiles, so that for better readability the definitions could be spread around more than one file.

Hardcoded, the above would look like:
Code:
<Hotkey 2>
<Toggle>
  <SendLabel w1>              
  <If ActiveWinIs WoW1>          
          <Key %trigger%>
  <Else If ActiveWinIs WoW2>          
          <Key ctrl alt u> 
  <Else If ActiveWinIs WoW3>          
          <Key alt shift u>
  <Else If ActiveWinIs WoW4> 
          <Key ctrl alt shift u>
  <Else If ActiveWinIs WoW5> 
          <Key ctrl u>
<Toggle>
  <SendLabel w2>
  <If ActiveWinIs WoW2>          
          <Key %trigger%>
  <Else If ActiveWinIs WoW1>          
          <Key ctrl shift u> 
  <Else If ActiveWinIs WoW3>          
          <Key alt shift u>
  <Else If ActiveWinIs WoW4> 
          <Key ctrl alt shift u>
  <Else If ActiveWinIs WoW5> 
          <Key ctrl u>  
<Toggle>
  <SendLabel w3>
  <If ActiveWinIs WoW3>          
          <Key %trigger%>
  <Else If ActiveWinIs WoW1>          
          <Key ctrl shift u> 
  <Else If ActiveWinIs WoW2>          
          <Key ctrl alt u>
  <Else If ActiveWinIs WoW4> 
          <Key ctrl alt shift u>
  <Else If ActiveWinIs WoW5> 
          <Key ctrl u>  
<Toggle>
  <SendLabel w4>
  <If ActiveWinIs WoW4>          
          <Key %trigger%>
  <Else If ActiveWinIs WoW1>          
          <Key ctrl shift u> 
  <Else If ActiveWinIs WoW2>          
          <Key ctrl alt u>
  <Else If ActiveWinIs WoW3> 
          <Key alt shift u>
  <Else If ActiveWinIs WoW5> 
          <Key ctrl u>    
<Toggle>
  <SendLabel w5>
  <If ActiveWinIs WoW5>          
          <Key %trigger%>
  <Else If ActiveWinIs WoW1>          
          <Key ctrl shift u> 
  <Else If ActiveWinIs WoW2>          
          <Key ctrl alt u>
  <Else If ActiveWinIs WoW3> 
          <Key alt shift u>
  <Else If ActiveWinIs WoW4> 
          <Key ctrl alt shift u>
..it looses its understandability a little, but should work