We were running running MongoDB atop EC2 instances. We chose to back MongoDB with EBS because that was the only reasonable way to get base backups (via snapshots) of the database. Although 10gen recommends using replica sets for backup, we also wanted a way to durably backup our database since there was so much important data in it (user accounts, billing, and so on).
On the other hand, we run PostgreSQL straight on top of a RAID of ephemeral drives, which has had good throughput compared to EBS so far. The reason we're able to do this is because PostgreSQL provides a mechanism for doing base backups safely without having to snapshot the disk[1]. Therefore, we just do an S3 base backup of our entire data (which uploads at 65 MB/s from within EC2) fairly infrequently, while doing WAL shipping very frequently.
You can either do LVM snapshots (with journaling) on the ephemeral drives, or use mongodump with the oplog option to get consistant "hot" backups. The downside of mongodump is it churns your working set.
On the other hand, we run PostgreSQL straight on top of a RAID of ephemeral drives, which has had good throughput compared to EBS so far. The reason we're able to do this is because PostgreSQL provides a mechanism for doing base backups safely without having to snapshot the disk[1]. Therefore, we just do an S3 base backup of our entire data (which uploads at 65 MB/s from within EC2) fairly infrequently, while doing WAL shipping very frequently.
[1]: http://www.postgresql.org/docs/8.1/static/backup-online.html