The ones you see on the top are mainly for use in business transactions for things such as filtering a business transaction by a specific cookie or header value, whereas the ones on the bottom (directly under web requests) are more for direct charting and alerting upon. I believe an important difference between the two is that the BT focused ones can't all be charted as they are basically stored just for constructing business transactions.
Note that when it comes to building a BT there's no reason you can't just use the standard web requests ones though it would be best to use the BT ones as that is what they are for. In several cases you'll be able to get the same behavior in a BT using either of them.
I would use the Standard web requests simply because, for them you can specify/filter for which application to use other than the first ones. In the first ones, application buttons are disabled yet i would like not to use all agents but the specific ones. May be there is a way it can be done in those ones for BT instead of the Standard web requests?
1. Specifically for BT, agents are disabled( cannot select)
Standard web requests are enabled(can select any agent group/application you want)