Add me to the list of people that feel like identifying the plant in question should come before considering removal.
I've read those "weed" websites and books and they are nutz.
Always idiotic to see tomato plants listed in a weed section.
And.... so many of the "weeds" have value in the garden as alternative vegetables and grains... plus the important wildlife value...
2 examples... leaving lambsquarter standing over the winter means that the songbirds have seeds to eat on those cold snowy / icy days...
and pokeweed...
Which produces berries for the songbirds... and for me, keeping the songbirds out in the garden means a reduction in pest bugs and stuff that would otherwise damage my munchies...
And then... there's a bunch of plants necessary to the butterflies in my garden as host plants....
Most plants have good qualities... learning what those qualities are means the difference between "weeds" and valuable additions important to the garden.
To answer the original question...
My answer is it depends on the plant.
If you post pictures of the plants in question, we can identify and suggest methods of removal.