a couple of sites I've used for finding and also advertising an apartment...
(I found these recommended in an online NZZ article about how difficult it is finding an apartment in Zurich, and where to look to stand a fighting chance. They recommended these as the places the Swissies look to find the places that go 'under the radar' and don't even get as far as being listed on homegate).

Ron Orp
www.ronorp.net

Separate sections for Basel, Bern, Luzern, St. Gallen, Zurich, Winterthur.

For Zurich, there's both german and english versions, but very few apartment ads actually get posted in the english section. Also sections for swapping apartments, etc.. (Look for the 'Dach über dem Kopf' section im the german version )


Jesselespool & Naloo's immomailing
www.jesselespool.com
www.immomailing.ch

Zurich-centric, as far as I know. Both offer the same service (and state in their AGBs that they share their sources).
For submitting an advert, this is free.
For searching, you pay a one time fee of CHF 50 to receive a daily email listing all the ads that have been submitted in the last 24hrs. They claim (but offer no guarantee) that their ads are not listed on homegate and the like. When submitting an ad, you have to check a box to confirm that you haven't also listed it on any of the big property sites, such as homegate.

I wasn't sure about this, but decided to give it a shot as I was getting desperate after the umpteenth homegate rejection!! I'm currently subscribed to jesselespool and get anything in the range of 0-10 apartment ads per day. Most of them are people looking for 'Nachmieters'. Also apartment swaps are often advertised here.


Tauschwohnung

For apartment swaps, you could also try www.tauschwohnung.ch. I haven't used it myself but I hear a friend has had some success using this site.

Hope these help...