Hi,
I just wanted to add an update for this topic, in case there are any concerned cat owners out there who are looking to bring their beloved felines to Canada.
We arrived safely on 01 October in Halifax. We were living in Germany and travelled with Condor (was part of Lufthansa, now part of Thomas Cook). For Germany - Canada, all we had to get beforehand were IATA-approved travel carriers plus their rabies shots (no follow-up blood tests etc. to confirm that the vaccinations worked).
In Germany, the cats were handed over to friendly - and thankfully cat-loving - ground staff. They took the cats to a special conveyor belt for pets so they could be scanned (presumably) and put on the plane separately. We gave the handlers a bottle of water for their water trays. The ground staff checked that we'd included an absorbent mat at the bottom of each carrier (we had) - airline regulation. Unfortunately I forgot to add the 'Bach Pet Rescue Remedy' drops that I'd specifically bought to add to their water (the airline said they couldn't be drugged, but special pet herbal drops were OK).
Advice: Cats can and will get wet during the flight (combination of water spillage / bathroom needs!). In hindsight, I would have put a disposable diaper / nappy in there as well to help, as they were damp when we collected them from the baggage area in Halifax. It was a chilly eve too, which didn't help, so I'd recommend bringing a couple of small hand towels with you to give them a rub-down as soon as you're clear of Immigration. We also took a photocopier box lid and a few handfuls of kitty litter in a plastic bag, to make into a temporary litterbox as soon as we got to the hotel (the security guys on the scanner in Germany were puzzled, until we explained we had 3 cats who would be needing the loo at the other end!).
Once we picked them up from a side room near the baggage area, a handler in Immigration checked their pet passports, general condition and charged us $46 in total.
All in all, it was a very smooth, well-managed process by the airline and ground staff. The cats were a little unsettled for 1-2 days before they got back to their usual eating / loo habits, but other than that, they're fine. I was definitely more upset than they were - my months of worrying about it were unnecessary.