Also, being one of the few big releases available for OSX I really fucking hate that Minecraft makes my fans go fucking mental after 5 minutes. I have a quad-core i7 laptop, Minecraft shouldn't rape it.
Office rental/lease/taxes - A lot of $
Electricity and Utilities - A hell of a lot of $
IT Infastructure and such- More cash (they might have this stuff but it needs to be maintained and upgraded especially in the case of a AAA title like this)
Development licensing for engines, middleware and such (all done on a case by case basis and costs more money.
Staff wages - Budget at least double what a staff member is worth on the team financially for unforseen circumstances that hold things up. At its peak, the team consisted of 42 full time and 5 contractors according to various articles posted around 2004/2005 so lets just say the average developer/artist wage was $50,000 there's $2million - double that for budgeting and theres $4million already. Notch couldn't even pay wages at $3m
Promotion and marketing - not cheap either. Some companies spend more money than common sense dictates on their marketing. A successful company like Sony spends £5m on Uncharted 3 - IN THE UK ALONE. If you look at Minecraft, that did phenomenal by word of mouth alone. Brink was heavily hyped and was a failure.
So yeah, $3m is a drop in the bucket of spending in games developement. You also have to realise that with the jump to HD the costs invariably go up. If you take Stacking, which was one of the best games of 2011 in my opinion, that cost $2m and was pretty short in how long it took to complete. If Psychonauts 2 was to be a fully featured game the spend would be a lot higher.
And Minecraft still wont be finished.
This Eurogamer/Digital Foundry article is also a great read with even more options that should suit you.
Hope this helps.
"The ideas at the heart of Warp are sound and, in general, the game is well paced and introduces its evolutions at just the right time. There's a looseness to the execution though, and it keeps the experience from becoming more than the sum of its parts. Warp is a pleasant enough diversion, but with patchwork design that remixes gameplay ideas and stylistic elements from sources as diverse as Splosion Man, Metal Gear Solid and Portal, it never gels into anything particularly memorable."
"While the sheer bombast has been toned down from the insanity of Uncharted 3, several of Vox Games' editors feel Uncharted: Golden Abyss is a better playing experience."
Really, it seems a bit odd that Kotaku are so negative.
Secret of Mana
Megaman X
Zelda: Wind Waker
Zelda: Links Awakening
Metroid Prime
Metroid Fusion
Final Fantasy IX
Prince of Persia 2008 (Which I can assume is never getting a sequel even though it shifted 2m+ units)