All Bosses from Zapdos come after a long dungeon and require you to go through another mini dungeon of 2 or 3 floors before you get to it. However there's a Save Point between the two dungeons if you wish to save and quit. It's also useful if you lose and don't want to go through over 1 and a half dozen floors again
Skarmory
The first boss you will meet is on the 3rd Mission where a Dugtrio comes to you asking you to rescue a Diglett. The Diglett is being held captive by this Skarmory. It requires some careful strategy and positioning to allow you to beat it but after a few well placed attacks, you should beat it easily
Blue Team
The next boss is a tricky one as it's the Blue Rescue Force featuring Gengar, Ekans & Medicham. They can put some quite powerful attacks on you especially if it's 2 on one. Using some of the explosive items you found should help you get them down a bit
Zapdos
The first "Legendary" boss as people will probably come to know it. Zapdos has a range of attacks, that sometimes do around 10 damage, sometimes up to 30 and if you use an explosive item on it when it's been weakened a little, it will bite back with a powerful thunder that does around 60 damage. Make sure you've got enough healing items and you should do fine. Be warned though as it's Pressure Ability will make you run out of PP for your attacks quickly.
Moltres
Moltres is the next boss you'll face, not too long after Zapdos so if you had trouble on Zapdos, I suggest levelling up a bit. Like Zapdos he has a wide arsenal of attacks ranging in Damage so just keep at it, the same strategy as before should work. As with Zapdos, it's Pressure Ability will cause problems if you're in battle for a while
Articuno
Articuno is a bit harder as you do not have the choice of going back to town to restock after defeating Moltres. However you should find enough items to tide you through within the dungeons before it. The same strategy as before should work on Articuno, but be warned as he can freeze you which renders you useless for a few turns wide open for damage
Groudon
After you have your new Force Hideout, you will then be able to go to one of the Volcanoes. After over 20 floors you will come across the usual mini-dungeon which at the end has Groudon. Groudon is a tough Pokémon to beat but if you have a powerful fused attack, it should be down in a couple of hits, however it can pack quite a punch so be weary
Massive Attack
While not a boss persay, this part of the Cloud Dungeon is really hard to complete. You will come across a room in the dungeon where 9 strong Pokémon will spawn. This will be an incredibly hard and time consuming battle. If yopu have link attacks that can take out two Pokémon at once...use it. Make sure you have some anti confusion items with you too as the Aerodactyls WILL confuse you repeatedly.
Rayquaza
A few more floors after that massive attack, you will be confronted by Rayquaza. He is a strong legendary Pokémon so be weary. It can Paralyze and Confuse so make sure you have remedies. Fused attacks are also a good idea here. After you beat it, he will stop the meteor and the credits will roll
Kyogre
After a massive 40 floor dungeon you will immediately come face to face with Kyogre. Kyogre can Freeze, Paralyze and Confuse you so be careful and it can give attacks that give out 100 damage. Again fused attacks should work if powerful enough.
Regirock
After a couple of missions you'll go in to a major dungeon which is 99 floors in total. On the 15th floor you will meet a Regirock. It will battle you. It can get in some major strong hits including explosions and be warned, there is a block in front of him which will disable one of your attacks when you step on it
Regice
In the same dungeon on the 25th floor you will meet Regice. It also will battle you. It can get in some major major strong hits including explosions and be warned, there is a block in front of him which will disable one of your attacks when you step on it
Registeel
In the same dungeon on the 35th floor you will meet Registeel. It also will battle you. It can get in some major major strong hits including explosions and be warned, there is a block in front of him which will disable one of your attacks when you step on it
Mew
Again not a boss persay but worth watching out for and it can pack a hell of a punch. Mew is elusively found on Floors 36-99 (only one floor each time you go through it) if you have the item that was obtained from the sands of the three Regi's forming. If you have it's Friend Area, when you beat it, it may ask to join you
Latios
The next boss is Latios. He is found after a 25 Floor Dungeon...he can pack quite a punch so be weary. Just some powerful attacks will take it out in due time
Entei
After rescuing Latias your next place of call is a Fire Dungeon, at floor 30 you will come across the Legendary Beast, Entei. It, being a Fire Pokémon gives powerful attacks that can burn so make sure you have some Burn remedies.
Raikou
Immediately after defeating Entei you are invited to a Thunder Pokémon filled dungeon, like with the others after 30 floors you will battle the Legendary Beast Raikou. It has some powerful electrical attacks that can paralyze you so be warned.
Suicune
Immediately after defeating Raikou you are invited to an Ice & Water Pokémon filled dungeon, like with the others after 30 floors you will battle the Legendary Beast Suicune. It has some powerful water and ice attacks that could leave you confusd and frozen.
Ho-oh
Right after you've defeated Suicune and gained the Rainbow Feather, you can go to another dungeon. This is a 40 floor big dungeon and has the Legendary Bird Ho-oh at the top. He packs quite a punch and can confuse and paralyze you
Jirachi
After beating Ho-oh and having Surf & Waterfall, you will be able to go to a massive 99 floor dungeon featuring Jirachi at the end. However this isn o ordinary dungeon. Your items will be removed so I suggest banking the important ones and your Pokémon will temporarily be reset to Level 1. When you get to the top you will battle Jirachi. He can give out a few powerful hits and confuse but is pretty easy to defeat if you have powerful attacks
Lugia
After becoming partners with Articuno, Zapdos & Moltres, visit them and they will open up access to a Level 99 Dungeon. You need Dive to go into this one however. After battling through the 99 floors you will battle the Legendary Bird Lugia. Now he has some pretty powerful attacks and can Patalyze you so be warned
Deoxys
Right after defeating Lugia you are invited to a 20 floor dungeon featuring Deoxys. However on each of the floors there is only one Pokémon, a Shadow version of any of Deoxys' forms, and you have to defeat it in order to turn the stairs on to go to the next level. Once you get to floor 20, Deoxys will battle you, he too has some powerful attacks so be weary and hit it with a few powerful attacks and he'll be down in no time
Mewtwo
After Ho-oh has joined you, a Blastoise & Charizard will come to you after being attacked by a Mystery Pokémon...you will now be able to go to this new dungeon...it is a whopping 99 floors big and has some pretty high levelled Pokémon so unless you're at a high level yourself don't enter. Once at floor 99, you will battle the Genetic Pokémon, Mewtwo can pack a bit of a punch once provoked however it's first few hits are fairly weak.

After you have defeated the bosses, if you have their Friend Area, you can go back and defeat them again and they may join your Rescue Force!

Is there more?