LogFAQs > #979404910

Assuming Crystal is not in discussion...

Gold has:
Mankey, Primeape
Growlithe, Arcanine
Spinarak, Ariados
Gligar
Teddiursa, Ursaring
Mantine
Ho-Oh w/Sacred Fire

Silver has:
Meowth, Persian
Vulpix, Ninetales
Ledyba, Ledian
Delibird
Phanpy, Donphan
Skarmory
Lugia w/Aeroblast

Primeape vs Persian
Persian has speed but not much else. Primeape is a rare fast fighting Pokemon that gets Cross Chop, which can come in handy for things like Red's Snorlax. Primeape wins.
Gold 1; Silver 0

Arcanine vs Ninetails
Both of these aren't as good as Typhlosion/Magmar who manage to get ThunderPunch to deal with Water Pokemon. I guess I'll give this to Ninetails though, with Vulpix getting Flamethrower at level 31 and evolving into Ninetails, while Growlithe has to be level 50 to get it (delaying evolution to Arcanine). Growlithe can just get Flame Wheel at level 34 and evolve then...but even with better Special Attack isn't outdamaging Ninetails. Ninetails wins.
Gold 1; Silver 1

Ariados vs Ledian
Ledian is weak to all of the elemental punches and is setup specially defensive, but at least gets some coverage moves in ThunderPunch and IcePunch (despite only having meh Special Attack) and has good speed. Ariados, while having better defensive types, isn't as fast (40 Base Speed Blows) and doesn't have access to the elemental punches. However, after taking care of the rockets in Mahogany Town, you get the Sludge Bomb TM...which gives it a Stab option. Not many noteworthy Pokemon are weak to poison though, and several resist it... So it's Ledian's Coverage Moves + Special Defense + Speed vs Ariados's better attack and Sludge Bomb... This is not an easy call. Due to being able to hit lots of weaknesses though with the Elemental Punches with Poison being meh as an offensive type, I will give it to Ledian. Neither Pokemon is all that good however...
Gold 1; Silver 2

Gligar vs Delibird
Gligar really got the short end of the stick offensively. It doesn't get Dig or Earthquake (outside Stadium 2) and for Flying only gets Wing Attack as an egg move. Delibird at least can use Icy Wind from Pryce and help with Claire and Lance. There are better users of the moves, but Delibird at least has some use. Gligar...just doesn't.
Gold 1; Silver 3

Ursaring vs Donphan
I want to like Donphan, really, but why can't it learn Dig? Having to make due with Mud-Slap until getting Earthquake just before the Elite 4 is just really bad... Ursaring on the other hand has huge Attack and Stab Return to destroy most things. It also can learn Earthquake and all of the Elemental Punches for coverage if you want (its special attack isn't that good, but they still have their uses). Ursaring wins.
Gold 2; Silver 3

Mantine vs Skarmory
Mantine gets easy access to a Stab Surf and an Ice Move in Icy Wind. Its Special Defense at 140 is stellar and its Special Attack and Speed at 80 and 70 are also usable. It has an Electric weakness, but smart people aren't leaving it in against Pokemon with such moves anyway. It's a great Pokemon that could help you the entire game, although is generally outclassed by Lapras or Feraligatr, who get stronger Ice Moves. Lanturn also is arguably better with an excellent offensive typing and trades Ice moves for Electric moves. Skarmory is very different. It is a defensive beast on the defensive side and gets access to a Stabbed Fly to handle most threats that can't hit it super effectively on the special defensive side. Steel type is also something. It is the best Steel type you can realistically get without trading. A pity that it doesn't get Steel Wing until level 49 or by TM. Both are good in their own way, but Skarmory has a stronger niche, so I will give it to Skarmory.
Gold 2; Silver 4

Ho-Oh w/Sacred Fire vs Lugia w/Aeroblast
Ho-Oh doesn't need Sacred Fire that much when Fire Blast exists...and has the same amount of power points and is effectively stronger (Att * Accuracy). Burn is also nice, but with most enemy mons not lasting long, it doesn't help all that much ingame. Lugia on the other hand really wants Aeroblast, as Fly isn't as strong. I also find Lugia to be more useful than Ho-Oh, with the Fire type not being as helpful as hitting with strong Flying attacks (which hit many of the same things super effectively). I'm giving this to Lugia.
Gold 2; Silver 5

So when all is said and done, I give it to Silver. Skarmory and Lugia w/Aeroblast are great in particular.