Software that works with S3 tends to work with competing APIs as well; just change a config option. Even if you’re interfacing with the API directly (you probably shouldn’t do that—use some sort of abstraction layer instead), there are open source alternatives that support the exact same API.
SQS can be useful for getting data out of AWS without worrying about whether your callbacks are down. For example, if you’re using SES, you might want to know when emails bounce; you can have all those events sent to SQS, then pull them out whenever and store them in something more generic. I don’t think it’s particularly common to use SQS beyond that.
DynamoDB—is that even still a thing? Isn’t Cassandra basically DynamoDB 2, but open source?
Aurora is expensive and makes exporting data a pain. I have no intention of using it until it’s easy to set up external replication so I can fail over to other providers (or leave). No external replication, no business, especially at that price point. Aurora was quite a disappointment.
Beanstalk is another one of those things that nobody actually uses. That being said, it doesn’t really lock you into anything; it’s just a way to automate some basic AWS tasks, really. But it’s generally more trouble than it’s worth.