You talkin to me?
ALL of them have motor mount issues (speeds and regular 3's alike, its the same mount between the two

). The side mount is just a flawed design, and tends to fail quite frequently. They are cheap though, and mazda has redesigned it. You can get a reinforced version through mazdaspeed motorsports, but from what I hear its not actually that much stronger.
If you are looking at autos, stay away from the 4 spd, they had all sorts of troubles. 2006 they introduced the 5 spd auto that significantly improved fuel mileage and reliability.
The AC IS weak, mazda introduced a diffuser that helped things a bit in 2005 that can be retrofitted to any of them (as can a cabin air filter) but its still a full black interior, so you shouldn't expect it to cool down right away anyways.
They also tend to have PCV valve problems from what I hear, although I've never had an issue.
I frequent mazda3forums.com, and its ok, although its a bit juvenile sometimes.
There are no really big functional differences between the current car and 2004 though. I drive an early build '04 and haven't had many problems at all (just hit 93k miles). It was restyled a bit in 2007. If you are looking at a car with nav, you want one before 2006, as you can't do ANYTHING on it when moving 2006 and later. There was a special edition car in 2005, that wasn't really all that special (other than you could get it with an ugly brown interior).