I was looking at pretty much the same choices as you when I was shopping. Drove the CR-V a couple of times and really wanted that, then swung over to the Toyota dealership just to look. I drove the Matrix first, which I LOVED. Tons of go and super quiet inside. With the seats down, I could fit Meg's crate in the back (though just barely). While chatting, the dealer mentioned they had just gotten a Rav-4 in that I could look at. Less than a year old, 8k miles, came with a set of new snow tires. Woman had purchased it from them originally and was moving to NYC, so she sold it back to the dealer. I wound up going home with the Rav, as they gave me a much better deal on my trade in than Honda would offer.
I've been really happy with the Toyota (no recall as mine is a 2008). Gas mileage seems great (coming from a full sized Silverado and Tahoe before, so that's not saying much perhaps!), it's pleasant to drive, great to park, and has done well on bad roads. The size has been great with Meg. I got really nice custom floor mats and seat covers, so it cleans up well even after a nasty weekend at a wet agility trial. More than enough room for the two of us, and I think I'll be fine if I add a second dog.