I made this batch script, so that I don't need to have a dozen of shortcuts on my desktop to launch Civ4BtS with mods.
I'll post it here, and if you find it useful... well, use it!
Instructions
1. Copy all the text in the following spoiler tag.
2. Open Notepad and paste.
3. Click File Menu, Save.
4. In the dialog box, there's a "Save as type" box. Select "All Files" in it.
5. In the "File name" box, type "Civ4BtS.cmd".
6. In the above, browse to your Civ4BtS folder, where your Civ4BeyondSword.exe is.
7. Save the file there.
8. On your desktop, right-click and select New, then Shortcut.
9. Browse to the Civ4BtS.cmd file you just created. Press OK and then Next.
10. Give it a name, e.g. "Civ4BtS". Click Finish.
11. Now the shortcut you created with have a very ugly icon. We're going to change it. Right-click on it, and select Properties.
12. Press the Change Icon button. It will prompt you that the file contains no icon. Press OK.
13. Browse to CivBeyondSword.exe. Select one of the icons displayed, and press OK.
And that's it. Now you can double-click the shortcut, and you will see this:
Type an option, and press Enter. Civ4BtS will then launch with the mod you selected. Press "x" to exit without launching, and "-" to launch without any mod.
The script dynamically generates the list when you run it, so you will never need to make changes when you add a new mod. The list of mods is sorted by name.
I'll post it here, and if you find it useful... well, use it!

Instructions
1. Copy all the text in the following spoiler tag.
Spoiler :
@ECHO OFF
SETLOCAL ENABLEEXTENSIONS ENABLEDELAYEDEXPANSION
:Setup
SET MOD_DIR="Mods"
SET CMD_LINE=Civ4BeyondSword.exe
SET MOD_LINE= -mod=
SET PARAM=
:ChooseMod
CLS
SET INDEX=1
SET CHOICE=
ECHO ============= Available Mods =============
FOR /F "tokens=*" %%i IN ('DIR %MOD_DIR%\*. /b /on') DO (
ECHO [!INDEX!] - %%i
SET OPTION_!INDEX!=%%i
SET /A INDEX+=1
)
ECHO ==========================================
ECHO [-] - Start without mod
ECHO [X] - Exit
ECHO ==========================================
SET /P CHOICE=Choose mod:
:CheckChoice
IF "%CHOICE%"=="" GOTO :ChooseMod
IF "%CHOICE%"=="X" GOTO :End
IF "%CHOICE%"=="x" GOTO :End
IF "%CHOICE%"=="-" GOTO :LaunchCiv
SET /A NUMBER=%CHOICE%
IF /I %NUMBER% LEQ 0 (
GOTO :ChooseMod
)
IF /I %NUMBER% GEQ %INDEX% (
GOTO :ChooseMod
)
:SetCmdLine
ECHO Launching !OPTION_%NUMBER%!...
SET PARAM=%MOD_LINE%"!OPTION_%NUMBER%!"
:LaunchCiv
START /B %CMD_LINE% %PARAM%
:End
ENDLOCAL
SETLOCAL ENABLEEXTENSIONS ENABLEDELAYEDEXPANSION
:Setup
SET MOD_DIR="Mods"
SET CMD_LINE=Civ4BeyondSword.exe
SET MOD_LINE= -mod=
SET PARAM=
:ChooseMod
CLS
SET INDEX=1
SET CHOICE=
ECHO ============= Available Mods =============
FOR /F "tokens=*" %%i IN ('DIR %MOD_DIR%\*. /b /on') DO (
ECHO [!INDEX!] - %%i
SET OPTION_!INDEX!=%%i
SET /A INDEX+=1
)
ECHO ==========================================
ECHO [-] - Start without mod
ECHO [X] - Exit
ECHO ==========================================
SET /P CHOICE=Choose mod:
:CheckChoice
IF "%CHOICE%"=="" GOTO :ChooseMod
IF "%CHOICE%"=="X" GOTO :End
IF "%CHOICE%"=="x" GOTO :End
IF "%CHOICE%"=="-" GOTO :LaunchCiv
SET /A NUMBER=%CHOICE%
IF /I %NUMBER% LEQ 0 (
GOTO :ChooseMod
)
IF /I %NUMBER% GEQ %INDEX% (
GOTO :ChooseMod
)
:SetCmdLine
ECHO Launching !OPTION_%NUMBER%!...
SET PARAM=%MOD_LINE%"!OPTION_%NUMBER%!"
:LaunchCiv
START /B %CMD_LINE% %PARAM%
:End
ENDLOCAL
2. Open Notepad and paste.
3. Click File Menu, Save.
4. In the dialog box, there's a "Save as type" box. Select "All Files" in it.
5. In the "File name" box, type "Civ4BtS.cmd".
6. In the above, browse to your Civ4BtS folder, where your Civ4BeyondSword.exe is.
7. Save the file there.
8. On your desktop, right-click and select New, then Shortcut.
9. Browse to the Civ4BtS.cmd file you just created. Press OK and then Next.
10. Give it a name, e.g. "Civ4BtS". Click Finish.
11. Now the shortcut you created with have a very ugly icon. We're going to change it. Right-click on it, and select Properties.
12. Press the Change Icon button. It will prompt you that the file contains no icon. Press OK.
13. Browse to CivBeyondSword.exe. Select one of the icons displayed, and press OK.
And that's it. Now you can double-click the shortcut, and you will see this:
Spoiler :

Type an option, and press Enter. Civ4BtS will then launch with the mod you selected. Press "x" to exit without launching, and "-" to launch without any mod.
The script dynamically generates the list when you run it, so you will never need to make changes when you add a new mod. The list of mods is sorted by name.