Reddit's default ordering ("hot") is to put the recently (last day-ish) popular stuff at the top, unpopular at the bottom. The amount of moaning that some members have on OcUK about content they think is unpopular would lead you to believe that would be ideal.
Of course, you can order it chronologically ("new"), or even use the fantastic "controversial" ordering where the stuff with the most votes - up and down - is at the top which is often where the real interesting and intellectual discussion is.
There's also "top" which is most popular of all time and "rising" which is number of upvotes per minute for things posted in the last hour.
Comment chains are still kept in the order they are made, though sibling comments are ordered in the same way that main threads are. There's no "jumping" to and fro because replies are kept next to the thing they are a reply to, unlike OcUK where everything is in the same list and you may find it a little tricky to work out who someone is replying to if they haven't quoted them.
Reddit's problem is also it's strength. The users. Memes, cats, more memes and reposts aplenty in the "default" subs - unsubscribing from them and subscribing to stuff that floats your boat improves the stuff you see immensely. Sack of /r/funny, /r/pics, /r/games. Nothing but karma whoring reposts and memes.