Game development during Rare's heyday was also quite a bit less intensive, required less resources, didn't require as many people, and was overall on a smaller scale. Not discounting Rare at all, just saying that Retro and Monolith Soft are working in a different era of videogame creation, so it's not really a side-by-side comparison. Rare was amazing back then, though. On the other hand, I agree with RolStoppable that Nintendo's inhouse development teams match them in quantity and surpass them in quality in the same time frame. 

Also, if we're talking diversity of content then ignore this but I would argue that Nintendo's Zelda team has had a pretty incredible run over the years. Some of the titles aren't as great as the others (talking about you, DS Zeldas!) but even an "average" Zelda game is a great/fantastic game by industry standards as a whole. The Zelda team has also been increasing its output with an average of nearly 1 game a year since 2006 while still retaining the high quality standards of the series. 

Rare were also a lot smaller though.

It's funny seeing all the Nintendo had a more impressive line up etc. But again, RARE was 1 studio, Nintendo comprised of multiple studios.

To have a fair comparison of what Rare did vs Nintendo. You'd need to count HAL, EAD etc all as completely separate entities.

I doubt we'll ever see a re-release of the original Grim Fandango, but just a few days ago Tim Schafer reinforced - see his answer to the last question in this interview - that he still hopes to get the rights to Grim Fandango and Full Throttle back from LucasArts Disney. As long as Schafer doesn't give up, I still have hope we'll see a proper Grim Fandango remake (i.e. in HD and with better controls) from Double Fine some day. BTW: I higly recommend Indiana Jones and the Fate of Atlantis, which is not only one of the best point&click adventure games ever created (# 4 in my personal top 10), but also the best original game based on a movie franchise in my opinion. It's much better than Last Crusade and it's available - exclusively afaik - on Steam: http://store.steampowered.com/app/6010/ .

You can easily find grim fandango on torrents. I was playing it last month until my laptop committed suicide.

Very true. But, Nintendo's various studios (many of which have staff swapping back and forth still today, and likely even moreso back in the day) also have 2, sometimes multiple, platforms to be developing for at the same time...between handhelds and consoles, and since Nintendo is a hardware manufacturer there are also transitions between hardware generations that take place which have obviously accounted for many delays, changes in development for many of Nintendo's games over the years. So, you're right :p but there ARE a lot of factors to consider...and as I said in my OP, it's just difficult to do a true side-by-side comparison. 

Well at least we can agree, that in their prime, all these companies have been awesome for gaming. I'm sure SEGA's AM2 studio etc would also be up there in their primes. Their contributions to gaming in the 90s were phenomenal.

Well for one thing, Rare was doing more than that years before, such as RC Pro Am, Snake Rattle n Roll and Battletoads.

But I would say other companies have had comparable or better stretches.

Nintendo for example. Old Capcom, from the mid80s through, I would say, probably the mid-to-late 90s.

RARE were better when they were Ultimate Play the Game! :D

The game that not only saved the SNES, but brought it to dominance. It is probably the first mega-hyped game ever made, and it really changed the tide of the 16-bit era, not just so that Nintendo caught up to Sega, but that Nintendo sales began to so heavily surpassed Sega that they ended the 16-bit generation quite a bit ahead of the Mega Drive.

While the N64 lost the generation, this game did save the console from dwindling into obscurity early on in its lifetime. While the N64 had Ocarina of Time, Mario 64, and Lylatt Wars from Nintendo, if you were going to play games with friends, there was a very high chance that it was going to be this one. The N64 without Mario Kart would have been an obscure system with a few forgotten gems without Rare. Luckily thanks to Rare, not only was there GE007, the most played game of the generation, but there were also a number of single player gems to accompany the first party games. GE007 was to the N64 in the West as Monster Hunter was to the PSP in Japan.

Anyway, there actually was a company that rivalled Rare, and their golden age happened to be the exact same time as Rare's, starting in 1994 and ending in 2001:

1994 - Final Fantasy 6, Breath of Fire, and Secret of Mana
1995 - Chrono Trigger, Front Mission, Seiken Densetsu 3, Secret of Evermore, Romancing SaGa 3
1996 - Super Mario RPG, Bahamut Lagoon, Gun Hazard, Treasure Hunter G, Tobal
1997 - Final Fantasy 7, Tobal 2, Bushido Blade, Final Fantasy Tactics, SaGa Frontier
1998 - Xenogears, Parasite Eve, Bushido Blade 2, 
1999 - Final Fantasy 8, SaGa Frontier 2, Legend of Mana, Front Mission 3, Chrono Cross, Parasite Eve 2
2000 - Vagrant Story, Final Fantasy 9, The Bouncer, 
2001 - Final Fantasy X

It started in 1991 with Final Fantasy IV, and Breath of Fire was made by Capcom, not Squaresoft. Squaresoft only acted as the game's publisher for its North American release.