I have both systems where there is an integrated IDE (Microsoft FrontPage against an IIS Development Web site with Visual Source Safe on all of the web content) and where there is not (java command-line development, Visual Studio Express Editions). An intermediate case that I use is jEdit 4.x with VSS integration via plug-in.
I think the integrated case is valuable for the reason it always is -- you don't have to leave your application to interact with source-control functions and you don't have to worry about remembering to add new files and to check out files before editing them. The ability to have a smooth work process and to minimize the risk of oversights is powerful, as far as I am concerned. Even when the IDE-plugin integration is less than perfect (the jEdit 4.x case), I still prefer it over not having it.
I also agree that having explorer integration on Windows, the case for Tortoise SVN, is also a great capability, even when IDE integration is available. This allows convenient operation without having to launch the IDE while also being able to launch from the explorer window into the IDE (depending on file type) or editor or make or whatever while operating in Windows Explorer.
And yes, the command-line interfaces remain valuable, especially for scripting of recuring-operation patterns.
I operate in many contexts. Having low barriers and fluidity of operation in all of them is to be prized.