There's are a few things I can think of that need to be fixed respecting Nestopia core emulation issues:
1. Young Indiana Jones Chronicles - "Screen shaking issues" V-Sync related I beleive. The topic has been discussed and updated recently here: http://nesdev.parodius.com/bbs/viewtopic...ba460988a90accb
2. Ninja Gaiden - During the intro animation-story graphic color glitch of the moon in the lower left portion. Also reported...
3. Castlevania - When defeating Medusa (prior to the last boss) sometimes you will receive the cross which destroys all enemies on the screen. Both issues 2 & 3 possible timing related bugs. Both noted here: http://forums.bannister.org/ubbthreads.php?ubb=showflat&Number=50410#Post50410
Those are the only NES game emulation issues I can recall. However, I believe there are other Famicom emulation problems.
I empathize with those who have sound desync/video desync/timing issues, although never experiencing them myself. I've played Nestopia on a variety of graphics cards, laptops and desktops, and I am lucky enough to only once to had a video issue on one laptop which was several years old, with Intel based graphics whose refresh was locked at 59. I simply had to change Nestopia from 60 to 59 and problem was solved.
All video cards from ATi Radeon 9600, 9800, HD 5670...To NVidia Gforce 7-series and 9-series cards, along with the aforementioned Intel graphics chips and more...No issues besides the above "problem".
I used Sound Blaster Live! card and the rest with variety of on-board audio with no problems.
Processors include: Pentium IV (1.4 GHz & 2.8) Northwood, Pentium Dual Core - various, Core2Duo - various, and i7 (Gen 2) 'Sandy Bridge' 3.4GHz...Again no problems.
My very limited controller experience, however, is just with the Saitek P880. Respecting that, I always use the default/Windows installed drivers and never add anything additional to them. All other 'controller' usage was via keyboard.
I've tried Nestopia under (32-bit) XP, XP SP2, XP SP3, Vista Home Basic & Premium, 7 Professional. Finally, also playing it under 64-bit Windows 7 home premium, no issues.
Again, I do empathize, but just never experienced any video/audio/timing issues myself.
While it may come off as bias, I believe the bigger interest should lie with fixing core emulation issues like those mentioned above, before all the different 'unofficial' attempts to try new video/audio/controller tweaking. Just my two cents...probably worth less in most places, and certainly people can spend their time doing whatever...lol.
EDIT: One other "bug" report I saw is fot the game Startropics 2 - Zoda's Revenge. The report states that when you're in world view (the view you take while traveling in the world), you can walk through walls and objects when you move towards the right.
Using the ROM with the following attributes: CRC: F8E6F5C8 and registers as Mapper 4 - dump "ok" (Not "bad") under Nestopia's launcher, I do not experience the issue.
I suspect the reporter(s) of the 'bug' may have a bad dump - or at least an 'alternative' one.