DP 51 (Cresselia) is currently missing. I can upload a picture for you later if you need it.
The 16 Pokemon Rumble cards are missing
http://bulbapedia.bulbagarden.net/wiki/Melee!_Pokémon_Scramble_(TCG)
We'll make sure to create that set link for the Tower.
The Multi Energy from the Emerald set is simply named "Multi"
Base set Chansey is spelled "Chansee"
Base set "Plus Power" has an unnecessary space. (Should be PlusPower)
Also, many cards with the name Pokémon in base set (and at least jungle) have a regular e instead of an "é"
Fossil has Raichu named "Raichu 498391"
Really nitpicky: Fossil: Should be "Mr. Fuji" (with the period)
Again, sorry if these are too nitpicky
Team Rocket set, "Here Comes Team Rocket" is missing the "!" and "Rockets Sneak Attack" is missing a ' (same with "The Bosss Way")
Gym Heroes
Old name --> Correct Name (I believe)
Mistys Seadra --> Misty's Seadra
Misty's Tentscruel --> Misty's Tentacruel
Rockets Hitmonchan --> Rocket's Hitmonchan
Rockets Moltres --> Rocket's Moltres
Rockets Scyther --> Rocket's Scyther
Sabrinas Gengar --> Sabrina's Gengar
The Rockets Trap --> The Rocket's Trap
Rockets Snorlax --> Rocket's Snorlax
Sabrinas Venomoth --> Sabrina's Venomoth
Sabrinas Esp --> Sabrina's ESP
The Rockets Training Gym --> The Rocket's Training Gym
Most of the Mistys, and Sabrinas need to be made Misty's and Sabrina's in this set. ( i was going to put the rest of the commons down, but that list was already long enough.)
Also, a neat feature would be to show what cards were legal in each year. i.e. What cards were legal in the 2008-2009 season; What cards were legal in the 2007-2008 season; what cards were legal in the 2006-2007 season ect...
But I like the unlimited view and the sorting sets from latest chronologically to earliest.
Edit: Also note that I only did up to Gym Heroes last time. I plan on picking up from there later.
Hopefullly this isn't too soon, but there are mistakes in Heartgold/Soulsilver
Farfetch D --> Farfetch'd
Pokeball --> Poké Ball
Pokegear 3 0 --> Pokégear 3.0
Pokemon Collector --> Pokémon Collector
Pokemon Communication --> Pokémon Communication
Pokemon Reversal --> Pokémon Reversal
Professor Elm S Training Method --> Professor Elm's Training Method
Professor Oak S New Theory --> Professor Oak S New Theory
Also, of the Prime pokemon, only Typhlosion has Prime in it's name. Not sure if it is needed in it's name since that's not part of it's name officially.