I like to pull out annual plants by their roots but clip perennials down to ground level  and let the roots stay in the soil until late spring. This way there is a chance a perennial will lie dormant all winter then come alive in the spring with fresh new growth. If you need more room for new plants don't feel bad about uprooting all sad or dead looking plants now. Life is too short to put up with ugly plants and we all need more compost so dead plants can be put to good use in the compost pile. Keep growing, Marianne Binetti