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Having a "Lib" folder at the same level as source projects is a common way.
To be honest, it's not the dependencies my projects have that I find hard to manage, it's the dependencies the dependencies have. I'd just like to mention NHibernate, Castle Windsor and the various Castle Windsor Facilities in particular. Getting all of those to play together on my last project cost me a lot of time.
For open source projects, I also like to have the source code handy because sometimes its useful to debug into the source code. (And sometimes because the documentation is so poor, you have to read the source code to find out how it works). I've seen VS projects arranged so that the project references the DLL yet at the same time, VS knows where to find the source code, as I write I can't quite remember how to do that.
So, a Lib folder for DLLs works for me; I often call it "Shared Dependencies".
As for open-source source code, I don't have a standard way to version that because each project is structured differently and has a different build process. I don't like to tinker with the open-source project structure or build method because then, I take responsibility for it. If for some reason, it won't build, or builds incorrectly, or produces a faulty DLL, the cause would be exceedingly difficult to track down, and I'd have to get deep into troubleshooting all of that which I dont care about at all.
In the office we have a share on the network for referenced asseblies. These could be 3rd party or assemblies of our own that could be shared between projects.
I also, don't like the idea of putting the dll files in source control. If all the developers have access to the share all will work fine.