There is no general standard or consensus, exactly like there is no general standard on leaving commented code in a Ruby file.
Generally, the idea of leaving stuff commented out is a bad habit from the days where we were used to code without a version control system.
If you are not using a Gem, there is no need to leave it there commented out. It's fine to comment it out temporarily while testing different behaviours with/without or temporarily for whatever reason, but once you reached a decision to take out the gem it's safe to remove it.
Personally, I generally structure the Gemfiles in the following way:
source 'https://rubygems.org'
# Rails core gems at the top
gem 'rake'
gem 'rails', '4.2.5'
gem 'sass-rails', '~> 5.0'
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.
.
gem 'responders', '~> 2.0'
# Gems, in alphabetical order
gem 'yajl-ruby', '~> 1.2.0', require: 'yajl'
gem 'bcrypt', '~> 3.1.0', require: 'bcrypt'
.
.
.
# Environment dependent gems, in alphabetical order
group :test do
gem 'database_cleaner', require: false
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end
group :development do
gem 'letter_opener', '~> 1.4.0'
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.
end
group :production do
gem 'clockwork', '~> 1.2.0', require: false
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.
.
end
group :development, :test do
gem 'byebug', require: false
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.
.
end