Here is your first script without the GOTOs, and a little simplified.
 Code:
;********************************************************************************
;*    Check To See If System Is A Server 	                                *
;********************************************************************************

$aOS = "Windows XP Professional","Windows 2000 Professional","Windows NT Workstation","Windows 7 Professional Edition"
IF ASCAN($aOS,$OS) = -1
   Exit 1
EndIf

;********************************************************************************
;*	Checking for Admin Rights on the PC					*
;********************************************************************************

Select
   Case $OS = "Windows XP Professional" AND EXIST("C:\Documents and Settings\xpadmin\ntuser.ini")
      $AdminRights = "1"
   Case $OS = "Windows XP Professional" AND EXIST("C:\Documents and Settings\Administrator\ntuser.ini")
      $AdminRights = "1"
   Case $OS = "Windows 2000 Professional" AND EXIST("C:\Documents and Settings\Administrator\ntuser.ini")
      $AdminRights = "1"
   Case $OS = "Windows 7 Professional Edition" AND EXIST("C:\Users\Administrator\ntuser.ini")
      $AdminRights = "1"
   Case 1
      $AdminRights = "0"
EndSelect

;********************************************************************************
;*	Module To Disable IE Reuse of Window When Launching Shortcut		*
;********************************************************************************

$IEWindowReuse = ReadValue("HKCU\SOFTWARE\Microsoft\Internet Explorer\Main","AllowWindowReuse")
IF $IEWindowReuse = "" OR $IEWindowReuse = "1"
   $nul = Writevalue("HKCU\SOFTWARE\Microsoft\Internet Explorer\Main","AllowWindowReuse","0","REG_DWORD")
ENDIF
And also an example of the second script you posted without using GOTOs.
 Code:
Break On
 
? "Adding Adobe JS Patch"
SHELL "C:\Windows\regedit.exe -s " + @ldrive + "\adobeJS.reg"


; ------- Determine if the user is in the LoginScript_QA group - Begin ------------------------
Global $Path
$QAMessage = "You are running the QA Login Script"

If @ScriptDir = @ldrive
   If InGroup ("LoginScript_QA")
      $Path = "qa\Netlogon"
      Call @ldrive + "qa\netlogon\login.kix"
      exit 0
   Else
      $Path = ""
   Endif
EndIf

If @ScriptDir = @ldrive+"qa\netlogon"
   $nul = MessageBox($QAMessage, "Message from Your System Administrator......",64,5)
EndIf
; ------- Determine if the user is in the LoginScript_QA group - End --------------------------


;   --------------- IDENTIFY SITE ------------------
;
;
; ----- Home Script  ------------------------------------------------------
; Created by:   10.10.2011
; 
; -----------------------------------------------------------------------------------
Global $ipaddress,$ipbytes[3],$site,$OS
$IPMessage = "Logon scripts are not currently supported on this system or in this location.  Script operation aborting.  Click OK to continue."
$sHome3 = "xxx"
$OS = @PRODUCTTYPE   ; Get OS for conditional scripting
 

; ------- Determine if the computer is a server - Begin --------------------------------------------------
$Computer_Name= Left(@WkSta,1)
If $Computer_Name <> "w" AND $Computer_Name <> "n" AND $Computer_Name <> "f"
   If $Computer_Name = "s"
      If AScan ($Server, @WkSta) <> -1
         Call @ldrive + $Path + "\Server\Server.kix"
         Exit 0
      Else
         $nul = MessageBox($IPMessage, "Kixtart Error",16,5)
         Exit 1
      Endif
   ELSE
      $nul = MessageBox($IPMessage, "Kixtart Error",16,5)
      Exit 1
   Endif
Endif
; ------- Determine if the computer is a server - End ----------------------------------------------------


; ----- Determine site by Domain Controller name or IP - Begin -------------------------------------------
$site = substr(@LServer,6,3)
$sitecheck = "xxx"
If AScan($Sitecheck,$Site) = -1
   $ipaddress = Join(Split(@IPADDRESS0," "),"")
   If Len($ipaddress) = 0
      $ipaddress = Join(Split(@IPADDRESS1," "),"")
   Endif
   If Len($ipaddress) = 0
      $ipaddress = Join(Split(@IPADDRESS2," "),"")
   Endif
   If Len($ipaddress) = 0
      $ipaddress = Join(Split(@IPADDRESS3," "),"")
   Endif
   $ipbytes = Split($ipaddress,".")
   If $ipbytes[1] <> xx
      $nul = MessageBox($IPMessage, "Kixtart Error",16,5)
      Exit 1
   EndIf
   Select
      Case AScan($axxx3, $ipbytes[2]) <> 0
         $site = "xxx"
      Case 1
         $nul = MessageBox($IPMessage, "Kixtart Error",16,5)
         Exit 1
   EndSelect
Endif
; ----- Determine site by Domain Controller name or IP - End --------------------------------------------


; ----- Call  System Wide Scripts for System Wide Changes - Begin ---------
Call @ldrive + $Path + "\System.kix"
; ----- Call System Wide Scripts for  System Wide Changes - End -----------



; ----- Call Main.kix for the user - Begin ----------------------------------------
If InGroup("xxx-Users")
   Call @ldrive + $Path + "\xxx\xxx.kix"
   If @error = 4		; Checks for forced exit of script
   Else
      ? "User Is Not A Member of the xxx-User Group"
      $nul = MessageBox($IPMessage, "Kixtart Error",16,5)
      Exit 1
   EndIf
Endif
; ----- Call Main.kix for the user - End ------------------------------------------


; Calls the printer script based on current site
Call @ldrive + $Path + "\" + $site + "\Printers.kix"
Exit 0
Not sure if any of the changed variable would effect your other called scripts, but you can atleast look at it as an example of how to do all the tasks without using the GOTOs. I think most people on this forum would agree that the GOTO code just makes the script much more confusing to follow/edit/debug.