I'm unclear as to what benefits I get from EBS vs. instance-store for my instances on Amazon EC2. If anything, it seems that EBS is way more useful (stop, start, persist + better speed) at relatively little difference in cost...? Also, is there any metric as to whether more people are using EBS now that it's available, considering it is still relatively new?
The bottom line is you should almost always use EBS backed instances.
Here's why
I'm a heavy user of Amazon and switched all of my instances to EBS backed storage as soon as the technology came out of beta. I've been very happy with the result.
EBS can still fail - not a silver bullet
Keep in mind that any piece of cloud-based infrastructure can fail at any time. Plan your infrastructure accordingly. While EBS-backed instances provide certain level of durability compared to ephemeral storage instances, they can and do fail. Have an AMI from which you can launch new instances as needed in any availability zone, back up your important data (e.g. databases), and if your budget allows it, run multiple instances of servers for load balancing and redundancy (ideally in multiple availability zones).
When Not To
At some points in time, it may be cheaper to achieve faster IO on Instance Store instances. There was a time when it was certainly true. Now there are many options for EBS storage, catering to many needs. The options and their pricing evolve constantly as technology changes. If you have a significant amount of instances that are truly disposable (they don't affect your business much if they just go away), do the math on cost vs. performance. EBS-backed instances can also die at any point in time, but my practical experience is that EBS is more durable.