You might be used to sorting messages in your Inbox, listing them by sender, for example, or the date they're received. In Gmail, you can do essentially the same thing by searching for messages. Searching may sound like more work, but it can actually be easier and a lot more powerful than sorting, once you learn a few tricks!
With Gmail's Unthreaded feature, you can now switch between conversation view, where a message and its replies are threaded together in a single conversation, and the traditional view, where replies are all listed separately in your Inbox.
Miss your nested folders? Use Gmail's Nesting feature to organize your labels in a hierarchy, the same way other mail programs let you do with folders.