If the organization is hierarchical, the ones at the bottom of the hierarchy may use this sentence for complaining. In those cases the "In a real organization..." remarks are not meant to be heard by the ones higher up in the hierarchy as they would most likely consider them insulting.
When used by coworkers as described above, this phrase can also boost the team spirit as it indicates that you have a common problem and suffer from it together. In these cases the form "If this was a real organization, we'd do/have something" is also common.
The word "organization" can also be replaced with anything that describes the environment more accurately: software company, library, warehouse, etc.
Example 2: "If this was a real IT company we would have a dedicated continuous integration server."
Example 3: "In a real library you'd have a dedicated shelf of sci-fi novels."
Example 4: "In a real organization you would've had a raise by now."