Okay, in the order that you can get them...
Phenac City
Makuhita, Lvl 30, Miror B. Peon Trudly
Bayleef, Lvl 30 , Mystery Troop Verde
Quilava, Lvl 30, Mystery Troop Rosso
Croconaw, Lvl 30, Mystery Troop Bluno
Pyrite Town
Noctowl, Lvl 30, Rider Nover
Flaafy, Lvl 30, St. Performer Diogo
Skiploom, Lvl 30, Rider Leba
Quagsire, Lvl 30, Bandana Guy Divel
Misdreavus, Lvl 30, Rider Vant
Slugma, Lvl 30, Roller Boy Lon
Furret, Lvl 33, Rogue Cail
Pyrite Bldg.
Yanma, Lvl 33, Cipher Peon Nore
Mantine, Lvl 33, Mirror B. Peon Ferma
Remoraid, Lvl 20, Mirror B. Peon Reath
Qwilfish, Lvl 33, Hunter Doken
Pyrite Cave
Meditite, Lvl 33 Rider Twan
Swablu, Lvl 33 Hunter Zalo
Dunsparce, Lvl 33 Rider Sosh
Sudowoodo, Lvl 35 Cipher Admin Miror B.
Agate Village
Hitmontop, Lvl 38, Cipher Peon Skrub
Mt. Battle
Entei, Lvl 40, Cipher Admin Dakim
The Under
Ledian, Lvl 40, Cipher Peon Kloak
Suicune, Lvl 40, Cipher Admin Venus
Gligar, Lvl 43, Hunter Frena
Stantler, Lvl 43, Chaser Liaks
Piloswine, Lvl 43, Bodybuilder Lonia
Sneasel, Lvl 43, Rider Nelis
Shadow Lab
Aipom, Lvl 43, Cipher Peon Cole
Murkrow, Lvl 43, Cipher Peon Lare
Forretress, Lvl 43, Cipher Peon Vana
Vibrava, Lvl 43, Cipher Peon Remil
Ariados, Lvl 43, Cipher Peon Lesar
Granbull, Lvl 43, Cipher Peon Tanie
Raikou, Lvl 40, Cipher Admin Ein
Realgam Tower
Sunflora, Lvl 45, Cipher Peon Baila
Delibird, Lvl 45, Cipher Peon Arton
Heracross, Lvl 45, Cipher Peon Dioge
Skarmory, Lvl 47, Snagem Head Gonzap
Miltank, Lvl 48, Bodybuilder Jomas
Absol, Lvl 48, Rider Delan
Houndoom, Lvl 48, Cipher Peon Nella
Tropius, Lvl 48, Cipher Peon Ston
Metagross, Lvl 50, Cipher Nascour
Tyranitar, Lvl 55, Cipher Head Evice
Snagem Hideout
Smeargle, Lvl 45, Team Snagem Biden
Ursaring, Lvl 45, Team Snagem Agrev
The Under
Shuckle, Lvl 45, Deep King Agnol
Outskirt Stand
Togetic, Lvl 20, Shady Guy
Now for some special info...
First, the three snaggable starters. In the beginning, you can only snag one, so pick the one you want to play through the game with; It'll be a while till you can get the others.
You can snag the second starter in Snagem Hideout. After beating the game, you get an e-mail from Secc. Go to Pyrite Town and battle Cail to find out the location of the second trainer. This will open up Snagem Hideout on the map. The Mystery Troop will be in the last room.
Now you can get the third one. You'll get another e-mail from Secc who'll send you to the Under. Battle Gurks (outside the junk shop) to find out the location of the last trainer; the Shadow Pokemon Lab. Also, while you're there, you'll be able to snag the Shadow Lab pokemon you missed earlier. The third Mystery Troop will be in the room where you fought Ein.
Once you get your third starter, you'll get yet another e-mail. This one sends you to the Snagem Hideout (and this is when you can catch Smeargle and Ursaring) When you beat Gonzap, you'll get the D-Disk. Use the disk on the UFO in the Under to find a new colosseum; the Deep Colosseum. The fifth boss in this series will have a snaggable shuckle.
After you have 47 snagged pokemon, you'll see TV broadcasts which lead you to the Outskirt Stand. Beat the trainer there and snag his Togetic.
Once you have all 48 pokemon snagged and purified, go to Battle Mode and beat all 100 trainers on Mt. Battle. (You can only use your pokemon from story mode!) When you win, if you have an empty slot on your PC, you'll get Ho-oh.
The Bosses and Their Pokemon
The Cipher Admins have some great snaggable pokemon, but they're tough to catch. Luckily, if you somehow don't catch them you'll fight each of the bosses more than once. But you really should get the pokemon on the first time you fight them, it's just easier that way.
And that's all I got. If I missed anything, please add to this.