Shaymin-EX from Roaring Skies
Combee from Plasma Storm
All I can really think of at the top of my head right now.
Edit:
I found some more that might help. I don't know if these are exactly what you're looking for, but here are what I found.
These are cards that return to your hand or deck, not switching with your bench, like Donphan and Kyogre-EX does, so I'm not exactly sure if the ones I found are the ones you're looking for.
Lopunny from Flashfire
Mienshao from Furious Fists
Tentacool from Primal Clash
Unown O from EX Unseen Forces
Well, I did find some that switch with your benched Pokémon, like Donphan and Kyogre-EX does, as well.
Here they are:
Riolu from Black & White Black Star Promos
Darkrai from Black & White Black Star Promos
Keldeo-EX from Boundaries Crossed
Gengar-EX from Phantom Forces
Dunsparce from EX Sandstorm
There are also two Aegislash cards from the XY set that lets you return them to your hand and switch them between one another.
Aegislash from XY (85)
Aegislash from XY (86)
Here are some Pokémon Pokémon cards that switch your opponent's active Pokémon with one of your opponent's benched Pokémon, instead of yours.
Druddigon from Black & White Black Star Promos
Gogoat from X and Y Black Star Promos
Swellow from XY
Swellow from EX Ruby & Sapphire
Krookodile from XY
Here's two unusual ones.
This
Blastoise-EX from the XY set and
Baltoy from the EX Sandstorm set lets you switch your Pokémon with one of your benched Pokémon, then your opponent does the same, after doing damage.
I am pretty sure these two cards are the only Pokémon cards that lets you do this with the exception of
Escape Rope, but that's not a Pokémon.
Edit: A moderator on PokéBeach.com edited all the links and put the PokéBeach.com links instead of the Bulbapedia links. I think that's really stupid since Bulbapedia is a huge site and it is well known and I use it all the time, but okay then. PokéBeach.com only cares about themselves and nothing else.
Another one.
Click the red + symbols to go to the Bulbapedia page about the card and click on the light blue link to go to the PokéBeach/Pokémon.com scan.
Edit: Celebi-EX from Boundaries Crossed+ lets you switch Celebi-EX with one of your benched Pokémon while doing 60 damage for 1 Grass Energy and a Double Colorless Energy (or two of any Energy).
Edit2: Bellossom from the new Ancient Origins set has an attack called Windmill, which deals 20 damage and lets you switch Bellossom with one of your benched Pokémon.
By the way, for some reason, there's no PokéBeach scan for this Bellossom. Guess it's because it's from Ancient Origins, the newest set. I hope they release scans of Ancient Oigins/Bandit Ring soon.
Edit3: Yanmega from HS Triumphant+ lets you deal 50 damage and switch it with one of your Benched Pokémon.
Edit4: Reuniclus from Plasma Blast+ has an attack that does 70 damage for one Psychic Energy and a Double Colorless Energy (or two of any Energy) that lets you switch Reuniclus with one of your Benched Pokémon.
Edit5: Lopunny from Flashfire+ has an ability that allows you to return Lopunny and all cards attached to it to your hand once during your turn.
Lopunny from Boundaries Crossed+ has an attack that deals 60 damage for 3 of any Energy that has your opponent switching his or her active Pokémon with one of his or her Benched Pokémon.
Edit6: Hitmontop from Furious Fists+ has an attack that costs one Fighting Energy and one Double Colorless Energy (or two of any Energy) that deals 4o damage and lets you switch Hitmontop with one of your Benched Pokémon.
Edit7: Azelf from Plasma Blast+ allows you to switch Azelf with one of your Benched Pokémon for one Colorless Energy, but it does not deal any damage.
Edit8: Talonflame from Roaring Skies+ has an attack that lets you draw three cards, and then switch Talonflame with one of your Benched Pokémon for one Colorless Energy.
Edit9: Kyogre-EX from Dark Explorers+ has an attack that costs one Water Energy and one Colorless Energy that deals 30 damage and gives you the option to Kyogre-EX with one of your Benched Pokémon.
Edit10: Emolga-EX from XY+ has an attack that costs one Colorless Energy that lets you search your deck for a Basic Lightning Energy and attach it to Emolga-EX. Then you switch Emolga-EX withone of your Benched Pokémon.
Edit11: Darkrai from Black & White Black Star Promos+ is a full art non-EX Team Plasma Pokémon that has an attack that costs one Darkness Energy and one Colorless Energy that deals 30 damage and gives you the option to switch Darkrai-EX with one of your Benched Pokémon.
Edit12: Shiftry from Next Destinies+ has an attack that costs two Darkness Energy and one Colorless Energy that deals 60 damage and lets your opponent switch their Active Pokémon with one of their Benched Pokémon.
Edit13: Bisharp from Noble Victories (76)+ has an attack that costs one Darkness Energy and one Colorless Energy that deals 30 damage and lets you switch Bisharp with one of your Benched Pokémon.
Edit14: Hydreigon from Plasma Freeze+ has an attack that lets you choose one of your opponent's Benched Pokémon with your opponent's Active Pokémon and deal 40 damage to your opponent's new Active Pokémon.
Edit15: Swablu from Triumphant+ has an attack that costs one Colorless Energy that deals 10 damage and lets your opponent switch his or her Active Pokémon with one of his or her
Benched Pokémon.
Edit16: Volbeat from XY+ has an attack that costs one Grass Energy that deals no damage, but acts as a
Lysandre+. It allows you to switch your opponent's Active Pokémon with one of his or her Benched Pokémon.
Edit17: Litleo from Phantom Forces+ has an attack that costs one Colorless Energy that lets your opponent switch his or her Active Pokémon with one of his or her Benched Pokémon. It deals no damage.
Edit18: Flygon-EX from XY Black Star Promos+ has an Ability that lets you force your opponent to switch his or her Active Pokémon with one of his or her Benched Pokémon.
Edit19: Masquerain from Primal Clash+ has an attack that costs one Grass Energy that confuses your opponent's Active Pokémon, and then lets you switch Masquerain with one of your Benched Pokémon.
By the way, I had to use
pokemon.com rather than
pokebeach.com for these thirteen last ones since I couldn't search for cards anymore on PokéBeach for some reason.