It's seems there's quite some confusion as to the difference between a "reply" on Twitter and an old school retweet (e.g. a tweet which starts "RT" but see note 1).

Ok, let's have a look at the difference and the implications...

In this scenario there are x3 people @Peter, @Paul, @Jane and @Mary. They all follow each other with the exception of @Mary (who only follows @Jane).

Note! I've made up these Twitter names! I'm sure @Peter etc exist but I'm just using them as examples here!

So, let's go through a scenario of tweets:

Peter tweets: "Jeez I'm hungry, what shall I eat for tea?!"

Paul notices this and decides to reply:

Paul tweets: "@Peter, fish & chips, the food of champions!" 

Note that this is a "reply" it is only visible to Peter (AND Paul's followers who additionally follow Peter) because it starts with @Peter's username.

Jane also notices Peter's tweet and, instead of replying decides to do an old fashion RT reweet and add a little reply on the end

Jane tweets: "RT @Peter Jeez I'm hungry, what shall I eat for tea?! <-- I'm hungry too - let's go out for dinner!"

From Peters perspective this doesn't make much difference as this reply still appears in his mentions column (a reply is just a mention which starts with username). 

However, for Jane's followers there is a BIG difference. ALL of Jane's followers will be subject to this conversation. Even people like @Mary who probably has  no interest in @Peter's dietary dilemma.

So, what's the moral of the story?

RTing instead of replying can be noisy and annoying so chose to use it when you REALLY want all of your followers to be subjected to it.

Notes:

*1 - The "RT" characters are arbitrary. There could be ANY characters between the username and the start of the tweet, e.g. sometimes you'll see ".@Peter Jeez I'm hungry, what shall I eat for tea?! <-- I'm hungry too - let's go out for dinner" - the fullstop at the front achieves the same result as the arbitrary characters RT - it turns the tweet from a reply to a mention.