As an example an app we built had a conflict between a jQuery plugin that the frontend devs had included, and a library that we had added with require. Having the conflict only show up in one place rather than the whole app certainly made it quicker to diagnose.
Addy Osmani's tutorials should be required reading if you're just starting out. [1] [2]
The only downside that we saw was that you will have to provide AMD versions of each library you use if you want to use jQuery from a CDN.
As well as being good practice it just feels really nice to have everything you're using declared at the top of the file you're in. The sugared require syntax helps with this. [3]
[1] https://github.com/addyosmani/backbone-fundamentals