here are the 3 best to my mind:

http://www.cafedusoleil.ch/

http://www.hotel-les-armures.ch/en/geneva-restaurant.php

Les Antiquaires

Suisse
entrée + plat: 30.- à 60.-

TEL: 022 311 24 ...
35 Grand-Rue Genève Genève 1204 46.20136 6.14666
1204 Genève

There is one just where tram stop 16 12 17 is

Chêne-Bougeries 2, Chêne-Bougeries, phone:             +41 (0)22 349 10 12    

Don't listen to these guys recommending "fancy" places. The cult place to eat fondue in Geneva is Bain des Paquis. Doesn't look like much but the fondue is excellent. For a more restaurant - type I would go to Auberge de Saviese also in Paquis.

The best fondue AOC is in Le gruyérien in Chêne-Bourg

Same for me, comparing all the ones people indicated here. It seems there's a new Gruyerien close to Pont du Mont-Blanc now...

Never against fondue (Bain des paquis)

Yesterday , we have been for our first time for Bains des paquis Fondue

The place is look like a shed , a lots of people and noisy , and my big surpris ,it is a self service fondue ???

Next time we will go Hotel des armures (for me the best place for fondue in Geneva)

Bains des PaQUIS FONDUE  is horrible !! :) never eat there again ! maybe fondue is good but  inside ,people and etc its awfull :) hahaha  but in Pl.eaux vives is nice restaurant better that bains

I think it's called "bergerie du gruyerien", it's beside the private bus depot not far from the lake.

It's sex on toast!