I know this is an old thread, but I wanted to comment:
I am a HUGE fan of both Age of Wonders and HOMM3. I've played the AoW series essentially since it's release in 1999 (missed out for a bit on AoW 2 which to this day I still don't consider a very good successor, but SM really knocked the bar back up and I've been loving it for nearly a decade now), and HOMM 3 not long after. The fact that even after all these years I still play the snot out of AoW, AoW SM, and HOMM 3 says a lot, I think.
So here's my verdict: They're both excellent, and they also both play quite differently. Basically the major difference is that AoW is large-scale, HoMM is small scale. AoW is more about empire building, casting spells that have major global impact and big, epic battles. Heroes is simpler, more about hero development and is usually pretty quick and dirty. That's not a criticism, by the way: Heroes is still a hell of a lot of fun and incredibly addictive, and has a lot of depth beneath its surface.
People have mentioned that AoW is more difficult. As far as campaigns go, I would say Age of Wonders is more difficult than Heroes 3, but easier than the campaigns in H3's expansions. Though like I've said, I have been playing the AoW series for over a decade so a newbie may not share my opinion.
I will say this: AoW SM seems much more balanced than HoMM 3. In competitive HoMM 3, I know that Conflux and Necropolis are usually banned for being too powerful, whereas Fortress and Tower are rarely ever played. While some races don't receive a lot of attention in competitive SM play (Frostlings, Halflings and Goblins tend to be the ones that don't show up very often), each race is a viable choice and has a decent chance of winning every map.
In the end, they're quite different games, but both are easily worth playing, especially at GOG's prices.
Though like I said, forget about AoW 2. It's rough, clunky, the balance is horrific (of the 12 races, four are ridiculously powerful and four are basically useless) and it's simply inferiour to AoW SM in every single way. AoW 1, however, is different enough that it's still worth playing in it's own right. I did a review on that one.