There are several types of train class in Italy, but the majority of trains have first and second class carriages. First class travel is not that much more expensive and I would recommend it for long-distance trains (particularly at festal and holiday periods) where trains are likely to be very busy. Having stood for five hours from Milan to Ancona, I wish I had splashed out a further 10-15 euro!
Long-distance trains are sometimes very busy, so it pays to board the train at the point where you are most likely to get a seat. The vast majority of stations will have a diagram for the constitution of these trains - you need to check these and stand near your preferred carriage. If you have a second class ticket, there is no point standing where the first class or the couchettes will stop.
Smoking is strictly forbidden on all Italian trains and buses. Despite the sometimes casual attitude of Italians towards various laws, the smoking ban is generally obeyed by the vast majority of people.
A very useful telephone number for visitors is the TrenItalia Helpline on +39 06 68475475. You must call from a foreign number (ie., it won't recognize VOIP systems such as Skype) and you should get an English-speaking operator between its opening hours of 0700-2100 Monday-Friday. The TrenItalia web site is undergoing transition at present, accouting for some anomalies in certain functions.