Please help me figure out how to get from Paris to Chamonix and back, via train.

I did this two years ago! I went from paris to Milano, then Milano->chamonix. Visit http://www.sbb.ch for the best route from chamonix. (Yup, the swiss trains are your best bet, and they don't seem to be linked up into the rail europe sites) Going via italy may seem a bit weird, but I found it to be the most direct in wintertime(snow and all that in the alps). Chamonix/mont blanc are right on the swiss/french/italian border, so it sort of make sense) There may be summer routes for the trains that are more efficient, but not sure about that. I had some random transfers, but they were pretty easy to figure out, and the net trip was cheaper than flying(and prettier!) Chamonix has local buses that are easy to figure out, and its pretty walkable, so don't worry about that bit. Annecy isn't on the right rail system, lyon may be. Annecy is soooooo pretty, but geneva is also rather stunning. (I'm typing on a droid, so can't link to maps, but hopefully the swiss rail site will get you moving along.)

Tried, http://www.sncf.com/? (what an awful site - it just keeps getting worse!) Never used rail europe, before.

Actually my route was cheap, not direct. Swiss trains might be worth looking into, but going to milano may not be the efficient way. Paris->Geneva is 3hrs, and Lyon should be about the same time. Have you tried visiting Chamonix.com? They list a bunch ofhttp://chamonix.com/access-and-transportation,9,en.html I've taken the mont blanc express(the train you'll need) from st. Gervais. Its privately run. And absolutedly gorgeous.

Use the http://www.tgv-lyria.com/main/FCK/File/site_fr/home/home_france_suisse.asp train to commute between Paris & Geneva. There are hourly shuttle buses from Geneva train station to Chamonix.

My recommendation would be to get the train to Geneva and then take ChamBus (apparently now called ChamExpress http://www.chamexpress.com) up to Chamonix. You'll need to get the train to Geneve-Cointrin/Geneve-Aeroport, not Geneve-Cornavin, since the bus leaves from the Airport. If your SNCF train from Paris goes to Geneve-Cornavin, you can easily catch another train to the airport - unless otherwise announced, most trains arriving in the Gare de Cornavin will usually have Geneva Airport as their final destination (if they come from elsewhere in Switzerland).

http://www.chamonix.net/english/transport/train/train_to_cham.htm, too, has some good info on getting to Chamonix by train. I traveled from Paris -> Chamonix many years ago, and I recall it took the better part of a day. Well worth it, though! Enjoy your trip.

http://www.bahn.com/ are always my go-to for booking trains anywhere in europe. For that route it will show you the train times but it seems they are not bookable online: Tickets can be purchased from any DB Travel Centre or DB-licensed travel agency or by calling the DB Travel Service on +44 8718 80 80 66 (chargeable).

Some years ago I took the "Mont Blanc - Chamonix Express" which goes from St Gervais up the Chamonix valley and over the hump into Martigny, Switzerland. (I managed to miss my stop, which was not the train's fault.)