Emulator

Have you tested this on the Virtual Console WAD in Dolphin? That would be helpful.

Is this game (and Master Quest) available for Virtual Console in the first palce? AFAIK, they were released only in a limited edition GC disc...

Yes, oot is on VC.

Oh yeah, the original game is indeed. Unfortunately, Master Quest is available only in the disc... since this issue still occurs in the latest builds, I'm thinking about this being related to the nature of the game itself (a ROM inside the disc). Would it be the case?

Issue 5826 has been merged into this issue.

Tried DSP LLE?
Tried single core mode?

I always use DSP LLE, but never considered using single core mode as a workout (besides when playing Soul Calibur II). Will give it a try after getting the emulator again (my HD was damaged beyond repair, so I lost quite everything I had...). I'll report here whether or not it works.

Tested just now with 3.5-393 using single core mode. This issue still occurs - only appeared later, but since it seems to be completely random, I wouldn't trust this.
I keep believing this is due to the game's nature - being a ROM running in an emulator that is built in the GC's hardware. Anyone else thinks the same?

I have the same problem, I have the PAL GC version of OoT+MQ and i tried different settings. The game freezes or Dolphin crashes after 3-20 minutes randomly. Would be nice if someone could fix this, I would even send the iso file if it would help. Best game

For me, the emulator didn't crash (yet), but the freezing issue seems very difficult, perhaps impossible, to know when and how many times it'll happen at each gameplay.

I've been playing Ocarina of Time (from the disk w/ Master Quest) and have been having the same problem with random crashing. I've tried a number of revisions -- currently using 4f13f6ecaa from 19/11/2013, and been able to duplicate the crashes as far back as a few revisions after 3.0 (further back than that and it becomes to difficult to get it to compile with modern libraries). Sometimes dolphin crashes completely, sometimes the emulation loops (no error messages, fps reported as 0), and sometimes the emulation crashes without taking dolphin down with it. The error I received from the last time the latter happened:

Non-recoverable Exception 2
------------------------- Context 0x80131cf0 -------------------------
r0 = 0x80ab90d8 ( -2136239912) r16 = 0x80119814 ( -2146330604)
r1 = 0x80146ab0 ( -2146145616) r17 = 0x80119820 ( -2146330592)
r2 = 0x8013e4a0 ( -2146179936) r18 = 0xbf05610b ( -1090166517)
r3 = 0x00000004 ( 4) r19 = 0x8036ead4 ( -2143884588)
r4 = 0x80131cf0 ( -2146231056) r20 = 0x8036dea4 ( -2143887708)
r5 = 0x8009f2ec ( -2146831636) r21 = 0x0000008a ( 138)
r6 = 0x8073ad48 ( -2139902648) r22 = 0x0000008a ( 138)
r7 = 0x8002b8c4 ( -2147305276) r23 = 0x0000033c ( 828)
r8 = 0x00ac66c0 ( 11298496) r24 = 0x8036ead4 ( -2143884588)
r9 = 0xdfffffff ( -536870913) r25 = 0x8036dea4 ( -2143887708)
r10 = 0x00000000 ( 0) r26 = 0x00000910 ( 2320)
r11 = 0x80100000 ( -2146435072) r27 = 0x8011fb20 ( -2146305248)
r12 = 0x00000357 ( 855) r28 = 0x8036ead4 ( -2143884588)
r13 = 0x8013d4c0 ( -2146184000) r29 = 0x800088b0 ( -2147448656)
r14 = 0x8036dea4 ( -2143887708) r30 = 0x00000000 ( 0)
r15 = 0x80119808 ( -2146330616) r31 = 0x8011fa60 ( -2146305440)
LR = 0x80ab90d8 CR = 0x40000088
SRR0 = 0x8009f2ec SRR1 = 0x00000030

GQRs----------
gqr0 = 0x00000000 gqr4 = 0x00060006
gqr1 = 0x00000000 gqr5 = 0x00070007
gqr2 = 0x00040004 gqr6 = 0x07060706
gqr3 = 0x00050005 gqr7 = 0x05070507

Address: Back Chain LR Save
0x80146ab0: 0x80146b18 0x80ab90d8
0x80146b18: 0x80146b30 0x8002d480
0x80146b30: 0x80146b78 0x800083f0
0x80146b78: 0x80146ba8 0x800057b8
0x80146ba8: 0xffffffff 0x80003274

DSISR = 0x40000000 DAR = 0xe7ac66c8
TB = 0x003f19edee15c946

Instruction at 0x8009f2ec (read from SRR0) attempted to access invalid address 0xe7ac66c8 (read from DAR)

Last interrupt (20): SRR0 = 0x8009eb14 TB = 0x003f19edee12785e

Things that often trigger crashes: day/night transitions (it often crashes immediately after the rooster crows), transitions between areas, killing an enemy (for the first time in that are), falling from a high place. The probability of a crash occurring builds up over time and persists across save state save/loads. E.g, if I've just loaded up the game normally (not from a save state), I can experience a few triggers without issue. However, if I've experienced many triggers since I last loaded normally, any additional trigger carries a very high chance of crashing. Since loading normally teleports Link to his house, I often try and reload from save states and do things slightly differently so I can keep playing, but it's fairly easy to get into a situation where nearly any area transition will cause a crash. If I load a save state and try to repeat whatever I did the first time to cause a crash, it will nearly always crash.

Sorry for my bad english
We have the same problem when in ocarina of time properties in game config check enable dual core then if you have ar codes and patches remove them and now I can go to kokiri village