Le Bouchon, in Carouge, offers both (Rue Blavignac 12). I have heard that the food is very good, including the homemade dips and fries, but the location does not seem ideal. This being said, if it suits picky lunch-goers in the Praille/Acacias area, it may very well be worth a try in the evening, too. You are not going there for the view, are you?

http://www.bouchon.ch/fr/specialites.html

I appreciate the Bouchon very much, I would recommend it.

This might be controversial but I quite like the Swiss Chalet restaurant at Plainpalais. Not just for fondue but also for other Swiss cuisine. Just ignore the Indian/Turkish/whatever waiters.

http://www.chaletswiss.ch/

Someone recommended the Auberge de Savièse tonight (Rue de Paquis 20, Geneva). Apparently, their Chinese fondue is delightful and the bourguignonne is great, too (about 40 CHF each, per person; all-you-can-eat option). For more info, visit their Website: http://www.aubergedesaviese.ch/

If you ever want grrrreat cheese fondue or other cheese-based specialties, I highly recommend La Table A Raclette in Saint-Julien (France) and Le Gruyérien in Chêne-Bougeries (CH). The latter has the yummiest meringues with double cream you will find outside of Gruyères! 

http://www.le-gruyerien.ch/

I second Auberge de Saviese.

thank you all for the advices!!!

And remember, the best way to enjoy it is outside on the terrace while it's still possible, so you don't get the smell allover you. If any of us receives an invitation we won't mind either