I have been trying to find out what compatibility issues still exist with PowerShell 3.0+ for older systems, I have read they can run side by side with PowerShell 2.0.
Which version of powershell / WMF should we be running on 2008, 2008R2, SBS 08/11?
What are the best practices around this?
If we do need to run PowerShell 2.0 on older servers, do we just keep out toolbox 2.0 compatible? (and in turn miss out on new features to accommodate all of our customers)
It isn't a question of OS compatibility; it's a question of application compat. Exchange Server 2010, for example, likes a specific version of PowerShell. So it depends entirely on what you're running on the server.
So, there isn't a "best way." You're going to have to research each product individually. Microsoft server products usually have a KB article about their PowerShell version. Other vendors may have something similar; they may not.
For side-by-side, you can't "specify." The application must be able to do so on its own. Most can't, meaning you can't install a version of PowerShell they're not compatible with.
Some applications don't care. SQL Server 2012 is pretty free and easy, for example.