Some of this is just speculation, but here is where I think Ash encountered his Hoenn Pokemon.
Episode: You Never Can Taillow
Location: Petalburg Woods
This one is easy, as any site you look at outright says Ash is strolling around Petalburg Woods (e.g. Bulbapedia )
Episode: Tree's a Crowd
Location: Route 104 (probably northern part)
This is a bit trickier, but not too bad. Ash caught Taillow in Petalburg Woods a few episodes earlier, but still hasn't reached Rustboro City before catching Treecko, so Route 104 is really the only contender. Of course it still takes place in a forest, so being Petalburg Woods isn't completely ruled out (part of the Japanese episode name is actually "Forest of Kimori", Kimori meaning Treecko, so he is presumably in some kind of forest).
Episode: Gone Corphishin'
Location: Dewford Town or Route 106
This is where the speculation really starts happening. A few episodes earlier Ash fought Brawley in a gym battle. As Brawley is the leader of the Dewford Town gym, that must have been his location then. A few episodes after catching Corphish, Ash is confirmed to be inside Granite Cave. So in between Ash can be assumed to either be around Dewford Town, or walking along the beach on Route 106 on his way to Granite Cave.
Episode: All Torkoal and No Play
Location: Route 111 or Route 112 (?)
Torkoal's location is listed in the anime as "the Valley of Steel". Unfortunately this location doesn't appear in the games. To make it even harder, Ash appears all over the place before and after this episode. Just before it, he is in Lavaridge Town fighting Flannery, and just after it he is in Mauville City. The obvious solution is Route 111, which runs between Lavaridge and Mauville Cities. However, it could still be Route 112 or the Fiery Path. Is probably isn't the Fiery Path, though, as its in-game appearance is completely different.
Episode: Let It Snow, Let It Snow, Let It Snorunt
Location: Shoal Cave ???
Snorunt's location is even more of an issue than Torkoal's, as Snorunt was found in an area that heavily snows. In the games, Hoenn has no such area, as it has a very tropical climate. In fact, the only place where you can even find Ice types is Shoal Cave. So, instead let's look at episode placement. Nine episodes beforehand, Ash battled the Mossdeep Gym, and then 2 episodes after catching Snorunt he battled the Sootopolis Gym. That gives a general idea of his whereabouts at the time, which actually is in the same vicinity as Shoal Cave. I truly believe that Snorunt's location, out of all of Ash's Hoenn Pokemon, is the one whose location is impossible to pinpoint in the games, but Shoal Cave is probably the closest you will get.
Like I said before some of this is just speculation, and some is even only guess work. The first few have pretty solid reasoning, though.
Sources: Episode Lists for Advanced, Advanced Challenge, and Advanced Battle Anime seasons, as well as the Bulbapedia pages for Ash's Pokemon.
As a side note, if someone wants to try and correct me and say "What about Aipom?", then Aipom was caught at the Indigo Plateau in Kanto, and wasn't in Hoenn at all, so I don't count it as one of Ash's Hoenn Pokemon. It played a greater role with Dawn in Sinnoh, anway. All other comments or criticisms are welcome, though.