Replies set the cornerstone of Twitter’s communication capabilities. We use them every day in hopes of making new friends or keeping up with old ones.
A few months ago, Twitter made some changes to their @reply system that prevented people from seeing conversations out of context. Everyone freaked out and Twitter clarified on their changes. I personally like the changes Twitter made.
Now I just wanted to give everyone a quick refresher on the current status of how @replies work. I feel like I regularly come across other Tweeps having trouble following conversations on Twitter.
The Basics
Twitter’s @replies still follow a lot of their originally proposed functionality. One of the main things a lot of people forget is that when you click Twitter’s “swoosh” 
button, your reply is now directly associated with that tweet.
If you ever receive a reply that seems out of the blue, check Twitter for the “in reply to ..” text and click to see what the Tweet was a response to. Most popular Twitter apps also display the “in reply to ..” text as well. Remember that Twitter can only associate your replies to Tweets when you use the “swoosh” button. Once again, most of the more popular Twitter apps have also embraced this functionality so there are no excuses.
Replying to people in this manner will prevent your reply from showing up in other people’s timelines when they are not following the person you are replying to. This becomes especially useful if you find yourself replying to people all the time and you are worried about posting too often. In short, it is an easy way to filter out the noise.
However, just because you won’t see conversations out of context in your friend stream, doesn’t mean you can’t hop over to Twitter search and view all public conversations taking place. In fact, Twitter Search can even thread your replies to help organize your conversations. If you are looking to see threaded conversations in a normal Twitter-like environment you should check out TweeTree which also displays videos and unshortens links.
Mentions
Mentions were adopted by Twitter when people started using @replies to reference other Tweeps in their tweets. The difference between replies and mentions is that when you mention someone you might not be talking directly to them. In this case, all of your followers would see your Tweet regardless of whether they are following the person you are mentioning or not.
Mentions won’t have the “in reply to ..” text because they are not necessarily directed at anyone.
Advanced Tweeting
You will regularly see people adding a . (period) before their @replies or placing some other text before the @reply to prevent it from becoming a semi-private conversation. It’s not always needed however there are times when you may wish to reply to someone and you want ALL of your followers to see the conversation taking place.
Remember that in the end, you can use Twitter however you damn please.
– Photo by db*photography