I'd say tops in this order:
1. Asus
2. MSI
3. Gigabyte
I've had more issues from Gigabyte (historically) than MSI. However, their boards of the past couple of years have gotten really good reviews. So, if I had used them more recently, I might put them above MSI. I don't think anybody could put much (taking in all history) could put anybody above Asus.
But really, it'd be best to look at individual reviews, motherboard by motherboard. For instance, if you find a board that has been around for at least 3 to 6 months, yet no reviews are out there, it's probably not worth messing with (my opinion) - the good ones will be reviewed by somebody at some point in time.
Also, I have had no bad experience with a generic Intel board, as far as stability. I'm not as crazy on functionality as I am the prior mentioned 3. For instance, I've got one Intel board right now that I got b/c it specifically fit the needs of a system that wouldn't be used very often - media center toy, really. Every time I turn the thing on, it beeps at me only b/c that's the only setting - always beep - no options to turn it off, and it's an onboard speaker, so I can't just disconnect it. Also, the thing always checks for a monitor, telling me "no monitor found" when I've got a tv hooked up via hdmi. So it just doesn't see anything on the VGA or DVI ports, and is telling me (though if no monitor, I couldnt' read it anyway) that no monitor is attached. To me, that's really annoying. The board runs stable, no issues, but still just annoying.
I've had problems personally, and fixing for other folks, with ECS and Biostar. Trying to remember whether I've ever used Chaintec, but from what I've read, they seem to be in the same boat with those.
There are other options out there as well. You could, for instance, just do a search on NewEgg based on features you want, and sort by reviews, and then see if there is one or two that spark your interest. Then do some online searching for the particular model(s) of your liking, and go from there.
Right now, based on all I've seen building and fixing, if I had no specific lead on a specific motherboard, I would be looking first for Asus, and then everything else. So when I do my search online for boards, I'd first look for features. If I find 2 or 3 boards that are about the same, I'd then look at brand and price (and specific board reviews of course), and balance it all out. Something like: Yep, I like this one being an Asus, but the MSI is only missing one feature (that I wouldn't use), and costs $100 less - so I might go MSI.
Anyway, long story short - don't just stick with one brand. I have had bad events with Asus boards as well, just not as frequent as others. MSI, that I can remember, I've had 0 issues with, but they are generally not as feature-rich, and the most recent reviews I've seen, they don't perform quite as well. Then again, the performance gaps on motherboards are usually so small that it isn't worth discussing.... unless you get into overclocking.
happy reading
"But thanks be to God, which giveth us the victory through our Lord Jesus Christ." 1 Corinthians 15:57