Batch Script - Parenthesized echo of the word "Where" issue

You have misdiagnosed the problem - WHERE has nothing to do with it.

You simply need to escape the closing parenthesis:

@ECHO ON

(
    ECHO [System.IO.DriveInfo]::GetDrives(^) ^| Where {$_.Name -like "C:\"}
)>> Outfile.txt

PAUSE

Here is one other option for you. This doesn't require you to escape the parentheses or the pipe. When you redirect the NUL device to the SET /P command it writes the prompt string to stdout. The one caveat to this is that SET /P doesn't write out a carriage return and line feed so you need an empty ECHO. to output the CRLF.

@ECHO OFF

(
<nul set /p "=[System.IO.DriveInfo]::GetDrives() | Where {$_.Name -like "C:\"}" &echo.
echo another line
)>Outfile.txt

notepad Outfile.txt
PAUSE

For what it’s worth, it seems that, after a ), CMD interprets ^| as |:

C:\> (echo 1.The && echo 2.quick && echo 3.brown && echo 4.fox) ^| find "q"
2.quick