You can just use the text you want to append followed by your variable generally.
C:\>set MY_VAR=Hello world!
C:\>echo #%MY_VAR%
#Hello world!
C:\>set MY_VAR=#%MY_VAR%
C:\>echo %MY_VAR%
#Hello world!
If you're just doing echo, that's fine. echo #%%j will do what you need.
But if you want to set the line to a variable, you have to enable delayed expansion. Add setlocal ENABLEDELAYEDEXPANSION to the top of your file and then surround your variables with ! instead of %. For example (and notice that I've added delims= to put the entire line in %%j instead of the first word on the line):
@echo off
setlocal ENABLEDELAYEDEXPANSION
set LINE=
for /f "delims=" %%j in (CMakeLists.txt) do (
set LINE=%%j
if "%%j"=="Extensions AntTweakBar" (
set LINE=#%%j
)
if "%%j"=="Extensions Inspection" (
set LINE=#%%j
)
if "%%j"=="Extensions InspectionBar" (
set LINE=#%%j
)
echo !LINE!
)
Given this input file:
Extensions AntTweakBar
some text
Extensions Inspection
Extensions What?
some more text
Extensions InspectionBar
Extensions InspectionBar this line doesn't match because delims= takes all text
even more text
The above script produces this output:
C:\>comment.bat
#Extensions AntTweakBar
some text
#Extensions Inspection
Extensions What?
some more text
#Extensions InspectionBar
Extensions InspectionBar this line doesn't match because delims= takes all text
even more text
And of course removing @echo off will help you debug problems.
But all that being said, you're about at the limit of what you can accomplish with batch string processing. If you still want to use batch commands, you may need to start writing lines to temporary files and using findstr with a regex.