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While no rail system's trains always run on time, Switzerland's are just about as close to that ideal as you can get. (In 2010, 96% of trains arrived within 5 minutes of their scheduled time, and 84% arrived within 2 minutes.) It is sometimes joked that the Swiss don't run their trains by the clock, but rather than they set their clocks by the trains. It is much more likely that your train will be on time than your flight.

A ten-minute transfer is quite reasonable, assuming that you keep your wits about you. Zurich HB is all on one level; to move from one train to another you don't need to climb up or down stairs or ramps, or wait for elevators. Just walk to the station end of your arrival platform (the tracks at Zurich all enter from the same side, and they all end at the station), walk across to the departure platform, and board the train. You can save a minute or two by knowing in advance which platform your connection train is departing from--check the SBB website before you go, and/or watch for announcements on the train before your arrive.

Getting to the front of the check-in line in 20 minutes may be a bit of a stretch. I haven't flown out of Zurich before, but I know that in general the queue at the check-in desk is sometimes zero minutes long, and sometimes it's a half hour or more. (And that doesn't count the time it will take to disembark from the train and walk across to the terminal.) On one memorable occasion, I found myself waiting for ages because the airline's two counters were held up dealing with an entire teenage football team, and a family with three dogs to check.

Overall, it depends on how many flights are leaving in the next couple of hours, and how well staffed (or not) the airline check-in counter is, and whether you have particularly good or bad luck. Airlines that are checking in multiple flights at the same counter will sometimes have floating staff near the back of the queue who will move late-arriving passengers to the front of the line (or will direct you to the shorter, faster-moving business/first-class line).

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Thanks kchadley. I already scoped out the train platforms and looks like there is a bank of check-in kiosks at the top of the escalator from the airport train stop. Those Swiss think of everything! Actually with the prospect of online check-in, etc, it might be a moot point, even with baggage. This is just the last leg of my return flight home, so if my bag doesn't quite make it 'til the next flight, it's not the end of the world.

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The check-in next to the train station is check-in 3. You can check in there if you fly SWISS. But also some other Airlines..

Check In 2 is about 5 minutes from the train station.

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Since you're starting in Milan, I'd be a lot more concerned about Italian efficiency than Swiss efficiency.

Hmm, Italian efficiency. Not a phrase you hear every day, is it?

One short section of track repair in either country and you might be in trouble. Personally, this is a gamble I wouldn't take--the stakes (presumably the cost of a new, last minute ticket) are too high.

If I were Murphy's Law, I would find your situation terribly tempting.

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I would take a train 1 hour earlier.
The fact is that Italian trains, especially the Cisalpino, arrive often late in Zurich.

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Copy from the electronic timetable of Swiss Federal Railways:

Milano Centrale - Zürich HB
EC 12 Milano Centrale - Zürich HB partly cancelled:
EC 12 from Milano Centrale departure 07:10 via Como S. Giovanni 07:45 - Chiasso 07:52 - Lugano 08:12 - Bellinzona 08:36 - Arth-Goldau 10:13 - Zug 10:29 to Zürich HB arrival 10:51 is cancelled between Chiasso and Zürich HB.

Replacement train operating Chiasso - Zürich HB with later arrival at Zurich.
Reason: Change to rolling stock

Duration from 04.07.2012 until 28.09.2012 from Monday to Friday.

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Even if this news doesn't affect your travel date, I hope it's un-nerving enough to encourage you to leave for Zurich the day before your plane departs--just to be on the safe side. If not...may The Force be with you.

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I would go to Zurich the day before- don't even think about trying this. While the reliability of Swiss trains is very good, the Milan to Zurich line is absolutely shocking- very unreliable.

Also, even on a reliable line, a 30 minute delay can happen easily (e.g. if a train is cancelled). Doesn't happen often, but does happen.

The key question here is what are the consequences of missing your flight? If you're easily able to pay for the cost of a new flight, go for it. If not, don't try it.

By the way, Swiss International Airlines has (despite their advertising) terrible service- you might easily have to join a considerable queue for check-in.

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Hey thanks all. Good catch on the EC12 cancellation. They really need to flag notices like that with a flashing red "!", not an innocuous blue "i".

Here's the rest of the story: I'll be returning from the Middle East on the Swiss flight and using a 30 hr layover to catch an opera at La Scala, so I wouldn't be able to get out of Milan 'til 10:30PM or so. Plan B would be to catch the late train to Chiasso (23:10 or 00:38) , Lugano, or Bellinzona (23:10) after the show (can duck out early if I really need to), sleep there at a station area hotel, and catch an earlier morning train to Zurich. Still not completely risk-free, but that will buy me an hour or two in the morning, eliminates the Italian factor, and gives me more alternatives. A bit more involved than I figured, but worth it for an opera fan like me.

Any suggestions between Chiasso, Lugano, or Bellinzona? I'd be stopping on the way down to check into a hotel and will have few hours to explore in the afternoon. Logistics-wise, Chiasso might be the smarter but boringer choice. Leaning towards Lugano based on the spectacular photos I'm seeing.

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I think you have no choice. You will hardly get the 23.10 train if you really want to enjoy La Boheme. Don't forget that you must first go by metro (M2 or M3) to the railway station, then to the upper level and finally to the platorm. So the only possibility wil be Chiasso. If you want to avoid any risk, you will have to leave Chiasso the following morning at 6.41, have breakfast in the dining car and change at Arth-Goldau (the corresponding train to Zurich will wait for sure).
Chiasso is boring, there is no doubt. The Como city bus runs up to the border, a few metres from Chiasso railway station, however.
You may also stop over at Lugano and put your luggage in one of the numerous lockers you will find there at the railway station.
Same remark for Bellinzona, if you like to visit the 3 medieval castles and the tiny medieval center (with 2 good and some other restaurants).

Hotels at Chiasso (Switzerland) and Ponte Chiasso (Italy): http://www.booking.com/
The closest hotel is the Touring, nothing to write home about, but clean and functional. Make sure that you can enter the house at 1.50am, however.

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Thanks again.

Yeah I'd have a hard time leaving La Boheme before the ending for sure, but this is Rigoletto and l'll be satsified if I can just hear Vittorio's Grigolo's La Donne e Mobile at the beginning of Act 3. It's all down hill from there... Fortunately I'll be in a box and can exit discretely without disturbing too many people. That should give me 45 to 55 min to get to Centrale, by taxi if need be. I'll been to Milan and La Scala before and have an idea of the logistics on that end.

So I'm thinking I'll try to catch the 23.10 to Lugano. I don't relish the idea of waiting around 90 min for the 00.38 then, as you point out, getting to the hotel at 2am.

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Sorry, I didn't know that you will travel in November. As to the end of Rigoletto, I agree with you.
It's fine that you can leave the Scala before the end of the piece. I think much will depend on the beginning time (8pm as stated or a little bit later as often in Italy and on the length of the entr'acte.
I don't think that you will need 50 min to get to Centrale. The official ATM site indicates 20 min (add some time for less frequent metro intervals and for the hike inside Centrale station):
PERCORSO sulla rete ATM e Nord Est Trasporti: parti da Teatro alla Scala, percorri 300 metri, vai alla fermata DUOMO M3, prendi la linea M3 (S.DONATO - COMASINA) per 4 fermate, scendi alla fermata CENTRALE FS, percorri 450 metri, fino a destinazione Stazione Centrale.
Tempo previsto 20 minuti

If you sleep at Lugano, check hotel Montarina (but not the backpacker section!), in a nice park above Lugano railway station. I prefer it to Federale.

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Thanks. I was about to book at the Montarina, but Continental Parkhotel in the same area came up for a lower price for a single room and looks even nicer (online anyway).

Also, how far in advance should I book the train tickets given the importance of keeping the schedule? The Milan visit will be early November. Should I book them now online, when I pass thru Zurich one week before, or the day of the Milan trip when I land in Zurich again?

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Continental is fine, it's usually much more expensive than Montarina.
Train tickets:
Seat reservation is neither compulsory nor usual in Swiss domestic traffic and in Italian regional trains like train 2686 Milano Centrale dp 23.10.
Lugano - Milano: reservation compulsory for direct EC trains (Lugano dp 13.48 and 17.48), neither necessary nor even possible for all others (most of them arrive at Milano Porta Garibaldi).
Buy the Milano - Lugano ticket either at Como SG (where you have to change trains if you leave Lugano at 14.28 or 16.28) or immediately after your arrival at Milano (at the ticket machine). Otherwise you may loose too much time before being able to board the 23.10 train. You can buy it at Lugano too (round trip ticket Lugano - Milano), but you will most probably pay more