I would include Guédelon rather than riding through vineyards.

http://www.flickr.com/photos/mksfca/4083925884/in/set-72157622755059630

To your list I would add the following:'

the ancient abbey of Fontenay;

the basilica in Vézelay, a beautiful building with considerable history. It's one of the starting points for the pilgrammage to Santiago de Compostela;

the Renaissance château of Tanlay;

the magnificent Gothic cathedral in Autun, along with the still-in-use-Roman theater on the outskirts of the town.

I think you could skip Chablis.

I wouldn't waste time riding a bike on those narrow hilly roads with improbable weather at this time of year. Vineyards are just rows of grape vines. Rent a car if you want to get out in Burgundy.

The best sights in Burgundy are the auberges with the most magnificent food and wine you'll find anywhere. Also visit the wine stores with degustation signs hanging above the door. There are a number of these in Beaune. Try the passetoutgrains, my favorite. It is a blend of pinot noir and gamay grapes.

While Guédelon is fantastic it is a big detour and will take time away from other sites. On your drive to Beaune from Paris I would try to stick to things that aren't too far off the autoroute to maximize your limited sightseeing time. All the places you and others mentioned are lovely and worth a visit but since you've only got two days (if you devote day 3 to Dijon) then you should focus on things that are near one another. I don't know if you'll have a car the night before you head to Beaune but if so I would suggest leaving Paris before 7AM. Get your breakfast at a rest stop on the autoroute and maybe some picnic lunch supplies. Certainly not high cuisine but if you are not in a larger town around lunch time (noon to 2PM) then your lunch options will be limited.

I'll suggest that you start in Noyers-sur-Serein and from there take the D11 most of the way to Epoisses (small town with a nice château) and then head on to Semur. You might have time on this day to wander on small country roads at random and just enjoy the countryside and small, anonymous villages that never merit a mention in guidebooks. I've spent time wandering in this area and here's a link to a trip report (with lots of photos) about driving in this area and visiting the places I mentioned plus other villages:

http://tinyurl.com/6dkeozh

As much as I love biking in the French countryside I agree with spaarne that your time on day 2 would be better spent using the car to see the countryside. Any of the other places mentioned that are in reasonable proximity to Beaune would be good visits for day 2 but it will require some driving. Châteauneuf-en-Auxois and the château of Commarin aren't too far from Beaune. I would also suggest getting picnic lunch supplies before heading off to maximize sightseeing time and save your restaurant meals for dinner.

If you want to drive through/past vineyards then on your way to Dijon from Beaune on day 3 head north to the town of Nuits-Saint-Georges and then from there pick up the small country road D122, starting in Vougeot, and follow that to Dijon and you'll see vineyards to the west and pass through some nice small towns/villages on the way.

And don't forget that you need the Michelin map of the scale 1:200,000. The map number for Burgundy (Bourgogne) is 519.

We were based in Beaune and never made it to Noyers or Epoisses, but did cover some of the same area suggested by FrenchMystiqueTours. His report on this area was very helpful to me in deciding where to try to go during our stay.

Here's what we did one day:

Drove from Beaune to Semur-en-Auxois on the D970 road.

After lunch there, took the D954 over to Alise-Ste-Reine/Alésia to see the site where Julius Caesar defeated the Gauls. There's a statue of Vercingetorix there, but not much else. Great view from the hilltop. A museum is supposed to open there in 2012.

From there followed a sign and took a little road to Flavigny-sur-Ozerain, a picturesque little hilltop town where the movie Chocolat was filmed.

Got back to D905 and followed it to near Sombernon where we headed south on D977b through Commarin and Les Bordes where we took a little road up to Châteauneuf. The views from up there are spectacular.

Went back down the little road, turned left and got back on D977b. In a few kilometers the road crosses the Burgundy Canal where we stopped to watch one of the large hotel barges going through a lock.

In another few km, just after passing under the A6 autoroute, we were back to the D970 and headed back to Beaune.

All the roads were in very good condition and well signposted. The 1:200.000 Michelin map was good to have. We do not have a GPS. Also encountered very little traffic.