Just as a comparison, if you take the top 25 (26 actually since the last few are tied) from Metacritic, which, conveniently enough means average scores of 90 or higher, you get:
1 Metroid Prime 2002 97
2 Legend of Zelda: Twilight Princess, The 2006 96
3 Resident Evil 4 2005 96
4 Legend of Zelda: The Wind Waker 2003 96
5 Legend of Zelda Collector's Edition, The 2003 95
6 Madden NFL 2004 2003 94
7
Soul Calibur II 2003 93
8
Viewtiful Joe 2003 93
9 Eternal Darkness: Sanity's Requiem 2002 92
10 SSX 3 2003 92
11 Madden NFL 2003 2002 92
12 Super Smash Bros. Melee 2001 92
13
Super Mario Sunshine 2002 92
14
Prince of Persia: The Sands of Time 2003 92
15
Metroid Prime 2: Echoes 2004 92
16 NFL 2K3 2002 92
17 Tony Hawk's Pro Skater 4 2002 91
18
Resident Evil 2002 91
19 Legend of Zelda: Ocarina of Time / Master Quest, The 2003 91
20 NCAA Football 2003 2002 91
21 Tony Hawk's Pro Skater 3 2001 91
22
Star Wars Rogue Squadron II: Rogue Leader 2001 90
23 NBA 2K2 2002 90
24
Pikmin 2 2004 90
25 Tiger Woods PGA Tour 2003 2002 90
26 Madden NFL 2005 2004 90
Since it seemed IGN was picking the best games on the GC irregardless of whether they were multiplatform or not, I'm surprised they left off Madden, Tony Hawk, and NCAA Football (which are on for the other systems I believe).
So far there's only 8 that are the same amongst the 20 IGN has picked. I'm sure it will end up being 13/25 in the end. Still, some pretty big differences (of course, I think the Zelda Collector's discs need to be excluded).
Wave Race Blue Srom has an 80 average on metacritic, making it tied for 112th with such games as Donkey Kong Jungle Beat and Baten Kaitos

. Tales of Symphonia is at 86, tied for 53rd and just above Fire Emblem PoR (avg. score: 85). Now certainly, you can't take the Metacritic top 25 as those scores are a bit skewed (too many Sports games and score were too high for early GC games just 'cause they were new and shiny at the time). So I recognize the desire to "reach down" and grab things like BW and DKJB. But I think IGN went a little overboard there on a few.
David, I've never played Eternal Darkness, but, like RE4, I would include it on my list (near the bottom for both) just because I recognize they are critically acclaimed - though I will probably never play either.