Shawn, we visited the Berner Oberland area last May and stayed four nights in Interlaken. Interlaken or one of the surrounding towns make great bases for the trips you are planning.

From Zurich, the train trip to Interlaken is a little over 2 hours. From Interlaken to the top of the Jungfrau is over a 2 hour trip also. Obviously, if you are starting in Zurich, this makes for a very long day sitting on a train. Bern is about an our from Interlaken and Zurich.

My suggestion --- stay in Interlaken, Lauterbrunnen, Wengen, or Murren. These are all easily accessible by train. The mountain views in Lauterbrunne, Wengen and Murren are incredible, but the convenience, hotel and restaurant selection in Interlaken are better. (We stayed at the Hotel Lotschberg in Interlaken, recommended in Rick Steves' book. Great place to stay!!!)

It depends on what kind of adventure you're looking for --- mountain hiking is available everywhere, Trummelbach Falls outside of Lauterbrunnen is incredible (and a great rainy, cloudy day adventure), and the boat trips on the two nearby lakes are beautiful. One thing I loved about Lauterbrunnen --- the waterfalls, cascading down into the valley, everywhere. Email me if you have questions.

Even if you have 3 days, you have time to enjoy a lot in Switzerland.
I have no hotel recommendations to make, but search the forum and I am sure a words of advice still exist on Zurich hotels. I stayed at the Welcome Inn close to the Kloten Airport. I cannot say I would go back. Most recommendations in the past suggest staying in town and taking the train from the main station to the airport.
The train station in the airport is well located. And Swiss trains are prompt.
If you want to go to the Jungfrau, I suggest you base yourself in Interlaken, Lauterbrunnen, or possibly Grindelwald, or even Wengen.
The trip is expensive, but if the day is clear, it is most impressive. I went last year and, were it not for the cost, I would gladly go back again this year.
The train for the Jungfraujoch leaves from Interlaken Ost train station. (Jungfrau gap literally translated, with Jungfrau being rendered variously as young maiden, young lady, and/or virgin.) The route up involves a change of types of train at Lauterbrunnen and Wengen. From Interlaken, the trip to the top will be about an hour. I suggest you go early to avoid the crowd, and, if you leave early enough, there is a cheaper ticket.
Getting to Interlaken from Zurich involves about a 2 and a half hour trip via Bern, which is the fastest way. I think the Luzern route is shorter, but takes longer in terms of minutes.

If you don't want to do the Jungfrau, the Schilthorn ride from Stechelberg via Murren, is quite nice. That is one of my objectives in September.

Another good trip is to take the train from Interlaken to Grindelwald. Then, after a short walk "up" the main street from the train station, take the gondola to a station called First. From there, walk to the Faulhorn Hotel. Great views all the way, both coming and going.
Also, a nice side trip is to Luzern.
We enjoyed it last year and plan to return this year for another look.
And yes, I do think you need to make a hotel reservation in Zurich. It is a busy town and the hotel/traffic ratio is not that favorable to the tourist.

OOPS another senior moment. The Jungfrau train change is at Kleine Scheidegg not Wengen. The train stops there, but the change of equipment is farther up the line at Kleine Scheidegg.
The length of the trip from Interlaken Ost is listed at 2 hours plus, about 2 hours, 18 minutes. It depends on the departure time. There is a Swiss train web site, the SBB as it is known. There is an English version. Good luck in your planning.
(I cannot really recommend hotels because we stayed for two weeks in two different apartments, one in Lauterbrunnen and one in Saas Grund.)

I just returned from 2 weeks in Switzerland, arriving and leaving from Zurich. In my opinion, if you are interested in the sights in central Switzerland you mentioned, you would not want to stay in Zurich. It is very easy to get to and from the Zurich airport on the train from any of the places you mentioned, but there is not that much to see in Zurich except expensive jewelry in shop windows. I think you would enjoy basing in either Lucerne or Interlaken, or the smaller villages in the Lauterbrunnen valley already mentioned. You would be staying amidst the most beautiful scenery imaginable, and would have a much shorter travel time to the other sights you want to see. I highly recommend the daytrips previously mentioned, as well as a boat trip on one of the lakes on either side of Interlaken or outside Lucerne.

Good afternoon, Shawn
I would suggest basing in Luzern as the
weather can be good in one place such
as Luzern and be cloudy in the Berner-
Oberland. Would plan the day by first
determining where it is clearer for the
day, if the forcast for the Jungfrau is
good, go for it. Also don't neglet the
Schlithorn if time permits. Also out
of Luzern you have trips up Mt. Rigi.
Titilis and Pilatus, the later can be
done easy in one half day, the other
two almost a full day each. Being in
Luzern you are only about an hour and
fifteen minutes from Kloten.
Richard of Hickory Hills, IL>

If you want to see the best of Switzerland, get out of Zurich. The clearest weather conditions in the Bernese Alps seem to be in the morning, which you may miss with this long trip. I would stay in Murren, Wengen, or Lauterbrunnen. If you want a more convenient location for daytrips, but with the sacrifice of not really being in the mountains, then Interlaken would be the choice (very very touristy though). Grindelwald is good if you want somewhere bigger but closer to the mountains (again touristy). If you really do want to stay in a city, then I would choose Bern or Luzern. Bern is going to be a faster trip from the Jungfrau area. It is a beautiful city, situated on a river. Luzern is even more beautiful, with a huge lake and many surrounding mountains. The train trip from Luzern to Interlaken is quite picturesque. With three days I would travel from Zurich to either Luzern or Bern and stop for a few hours, then head into the Jungfrau region, where I would spend the next two full days. Do a search and you will find lots of info below on good hikes and other things to do there.