We're travelling through Southern Africa at the moment, and slowly started looking into where in Namibia we can see meerkats. Strangely enough Lonely Planet doesn't mention meerkats at all, besides dedicating their whole cover of the Southern Africa guide to it. We are a bit flexible in the way that we can add Botswana to our itinerary if they're better visible there. I found a weblog of someone that went to Planet Boabab to see them, but there wasn't much info about it (like if it was a day tour and how expensive it was). I read that they need to be habituated, so options are limited. Does anyone know what the best place is to see them? And if it is in Botswana, is the shuttle to Windhoek still going once a week? Thanks for the info!

The tours from Planet Baobab are packages including accommodation and other activities and are pretty expensive ($500pp plus). You can't just pay $50 to visit the meerkats for a few hours. Details of the tours are here
http://www.unchartedafrica.com/page.php?p_id=322
Click on the rates link for prices.
A far more informal (and free) experience would be to visit the Rostock Ritz in Southern Namibia but these are "rescue" meerkats kept in an enclosure.
There are also a couple of operators in South Africa (Oudtshoorne) that specialise in meerkat visits
http://www.meerkatadventures.co.za/
http://www.meerkatmagic.com/

I should add you can of course see completely wild meerkats in any suitable terrain. You'll see them regularly anywhere in the Kalahari. They won't come and sit on your head though ;-)

You can see them quite easily in Kgalagadi Transfrontier Park in South Africa. I sighted them sometimes in my 6-days safari there.
Probably there are in Botswana side of that park too, but I've never been there, so I can't assure it.

Thank you both so much! We fly out of Cape Town, so these meerkat experiences are a lot easier to get to. Perfect! Decided to skip Botswana now, and have way more time suddenly! Thanks!

We spent two months last year in Botswana and Namibia. We saw a lot of ground squirrels which can be mistaken for meerkats, but no actual meerkats in the wild and that includes Kgalgadi. However, there is a campground called Trails Kalahari Rest Camp about 60 km from Twee Rivieren where the owner is a retired researcher. Now she cares for rescued meerkats - usually abandoned runt infants. They become her babies, so tame they sleep with her. They are affectionate and adorable. However, by the time they are adults they voluntarily move themselves out of her house and into outdoor burrows. Once they discover sex they are gone forever.
If you camp there, you have the opportunity to observe them at close quarters and it's a lovely experience.

Meerkats are much longer and leaner than ground squirrels and have very distinctive facial markings with pronouced black ears, eye rings and snout tips. They are also usually seen in large family groups whereas ground squirrels are usually alone or in pairs. Ground squirrels are very common frequenting places humans go such as rest camps and picnic sites (which meerkats won't do).
It is very possible to see meerkats in the wild though. I've seen then a few times southern Namibia but very regularly in KTP. So keep your eyes open. It's nice to see the habituated animals up close but they are absolutely fascinating to watch as a group in the wild.