Pokemon the characters have 

Pikachu, Nidoran, Rattata (traded for an Abra), Spearow, Shellder, Bellsprout, Magby (given by Bill, see Pokemon from Gold/Silver), Cubone, Vaporeon 

Onyx, Rhyhorn, Golem, Mr. Mime (female, named Mina), Kingler (briefly), Bellsprout (also briefly), Jynx (male, named Laurie, traded Kingler to get this), Ferneon 

She says she has lots, but the only ones we ever see are Espeon and a few others

Growlithe, Magikarp (bought from guy, traded for Oddish) 

Vulpix (named Sundance), Scyther 

Pidgeotto, Fearow, Doduo, Beedril, Ponyta (traded for Aerodactyl), Treagle (see column to the right), Seleneon 

Marowak, Gastly, Gengar, Ditto, Xerox, Jolteon 

Machamp, Hitmonlee, Hitmonchan, Mankey, Flareon 

Dragonair, Gyarados, Ampharos, Lapras
Glaciereon, Lapras, Seel, Piloswine, Psyduck, Shellder

New Pokemon in the fic 

Treagle: Flying/grass type, learns Fury Attack, Peck, a new attack called Fury Thorn (where the Pokemon fires thorns at the opponent), can learn Fly and Cut, and probably some others.  In case you couldn't tell, the pic is an Articuno colored green, with an Oddish leaf crest on its head and a Victreebel's tail thingie. 

Sneezing: Evolved form of Weezing, and looks like Koffing except it has arms.  Can do same attacks as Weezing, and can also learn Strength and Fly. (see the image?  Those are Geodude's arms colored purple) 

Ferneon: Eevee with the Leaf Stone.  I edited that picture with the set from Fakemon, isn't it neato?  It's a green Vaporeon, with the tail from Oddish leaves, and ears from Weepinbell.  It learns Vine Whip, Leech Seed, Razor Leaf, Tackle, Absorb, Solar Beam, Petal Dance, and some other grass attacks. 

Seleneon: Eevee with the Moon Stone.  Another Fakemon image, this was made using Hapinasu's (Chansey's GS evolution) ears, and Mokoko's neck-ruff-thing (see Denryuu, below)Its type is psychic/normal, and it knows Sing, Pound, Doubleslap, Metronome, Softboiled, Psywave, Psybeam, and some other psychic Pokemon attacks and attacks that the pink Pokemon (Clefairy, Jigglypuff, Chansey, etc.) learn.
Glaciereon: Eevee with the Freeze Stone, a stone I made up (it's basically a Water Stone encased in ice, and you have to use it quickly before the ice melts).  It's light blue/silvery, and it's kind of spiky like Jolteon, except ice spikes.  

Venodabra: This isn't a real Pokemon (like, it couldn't be considered one of the 251 known species), this is what happened when Aidan's Xerox fought against a Venomoth and a Kadabra both at the same time.  Xerox can transform into more than one Pokemon at a time, so that's how it did this.  It can do combination attacks too, like as a Venodabra it did Poison Beam (combo of Psybeam and Poisonpowder). 

Xerox: the evolved form of Ditto, which is Ghost/Normal type.  It looks like a see-through Ditto, and it learns Pound, Poison Gas, and Softboiled, as well as Transform.  You can't teach it TMs, though, and if you want to erase an attack you can't erase Transform. 

Tygra: Fire type, looks like a tiger with its fur on fire and a flame on the end of its tail.  Learns Fire Blast, Fire Spin, Ember, Slash, etc. 

Phantasmo: Ghost/Fire.  If I told you any more about this one it would spoil the plot, therefore, I won't. 

Whark: I didn't create this, it's sort of a...crossover.  Between Riven and Conclave.  Yep.  It's (c) Rand and Robyn Miller, I assume, because it's in the game Riven.  In Riven it's a rather bitchy sea creature, and you can summon it on Garden Island but if you do it too many times Wharky gets pissed and slams into the glass wall separating you and it (which never breaks, for some reason).  It also lives in the lagoon on Jungle Island and y'know that big conical structure hanging over the lagoon?  'S a Whark gallows.  Gehn drops people in there and feeds them to Wharky.  That's why when you go on that structure you hear a banging noise, that's the Whark asking for its dinner. ^-^ Here's a real image from the game of the Whark, I'll have a Fakemon image soon too. 

Sunner: Sunners are also (c) those cool dudes who made Myst and Riven, and they're from Riven.  They live on Jungle Island (that's the only place I've seen them, anyway) and they're basically like how I described them in episode 30: lazy.  They're kinda like Slowpoke: they sit around on the rocks all day, until you get too close to them.  Then they get scared and run away.  Here's an image from the game, but I'll be making my own...interpretation. ^-^ 

Ytram: Also a Riven creature, not mine.  This is a little orange/black/yellow frog, and you have to catch him on Book Island for some reason or another...*shrug* Guess it's so you can do the Stone Circle puzzle, but I figured that out without the help of the Ytram trap.  You catch 'em (in a vaguely Pokeball-shaped trap), they chirp, then they run away.  Eh.  I would say R and R were making an allusion to Pokemon with that but I'm not sure whether it was out or not at the time of Riven's development...I'd guess not.  Anywho, here's a pic of the Ytram from the game and there'll be a Fakemon one too, blah blah. 

Pokemon from Gold/Silver 
Cleffa: This is the pre-evolution of Clefairy, as in breeding Clefairy or Clefable results in this.  Its English name has now been announced, and it's Cleffa, so I have to go back and change the name in the fic.  Also (this is just in the fic, but I believe it applies to the game as well), it evolves into Clefairy with the Moon Stone. 

Ampharos: I don't know much about this guy except that it evolves from Flaaffy, who evolves from Mereep.  I assume it's dragon and electric type (cool combination, I think), because of Denryuu, its Japanese name (denki, the word for electricity, shortened to Den, and then Ryuu, the word for dragon).  And contrary to popular belief, the name is NOT spelled Tenriyu (come on, people, learn your katakana right).  

Buubii: The pre-evolution of Magmar, isn't it cute?  In the fic I'm naming it Pele, after the Hawaiian volcano goddess, but again this isn't the actual English name.  When I found out that the English name is Magby, I had that be its species name and Aoife just nicknamed it Pele.  I'm assuming (don't know for sure if this is true or not) that this guy is the result of breeding two Magmars, and that it evolves into Magmar with the Fire Stone.  Don't quote me on this, though.  

Chinchou: This is an "angler fish" Pokemon, and it's water/electric type.  It evolves into a thing that looks like a whale named Lanturn, and its Japanese name is Chonchii (and yes, Chinchou is its official English name). 

Ledian: flying/bug type, it evolves from the ladybug Pokemon, Ledyba.  It's kinda like a red ant with wings.  It's called the "many-thumbed" Pokemon, for whatever reason.