Independently structured congregations gravitated toward para-church movements as a secure ground for cooperative work.
Connectionally structured congregations used to find their outlet for cooperative work through bodies in their denominations.
Para-church groups focus on one area of Christian ministry. If they did otherwise they’d be a church. Which would mean they’d have to spread their focus to the full spectrum of life and ministry which a healthy congregation should embrace.
This is to say that para-church ministries are a tool, not an end in themselves.
A local church is an end in itself. It is a fulfillment of God’s saving purpose, not a tool for something more.
(Which is not to say that the church does not have purpose.)
A more contemporary phenomenon is the rise of those from connectional churches substituting the para-church for their denominations as the primary ground through which their cooperative activities are focussed.
This serves to fragment their denominations, which increasingly become congregational in function while still connectional in polity.
Something will, as they say in the classics, have to give.
Here’s 9Marks (the para-church group built around Mark Dever’s ministry) on the nine marks of a healthy para-church.
They give an insight into para-church ministries and some helpful internal critique, as well as pointing out that, as a movement that does not have a direct biblical mandate, the para-church should be marked by humility as it relates to the church.
Mark 1: A healthy parachurch ministry knows that it exists primarily to protect the church.
Mark 2: A healthy parachurch ministry makes a clear distinction between church and parachurch.
Mark 3: A healthy parachurch ministry avoids acting like the church.
Mark 4: A healthy parachurch ministry does not pressure the church to act like a parachurch.
Mark 5: A healthy parachurch ministry humbly heeds the history of parachurch movements.
Mark 6: A healthy parachurch ministry understands the difference between the pragmatic and the principled.
Mark 7: The healthy parachurch has a counter-cultural understanding of management and money.
Mark 8: The healthy parachurch maintains a strong commitment to, and understanding of, the gospel.
Mark 9: A healthy parachurch ministry seeks accountability relationships with the church.
mgpcpastor's blog 
Thanks Gary. I’ve been struggling for a while to get a handle on where the whole para-church thing is heading, especially as more gen-y Christians seem to want little to do with “church” in any recognisable or denominational shape. Student ministry and church planting both seem to be taking on a life of their own, independent from the church. I can understand many of their frustrations with denominational bureacracy, but I’m not sure the division of the church along parachurch lines (all students in one corner) is the answer.
Hey Douglas ~
There’s more I’d like to try and work through.
Suffice to say that (para-church or not), homogeneous unit principle groupings can be a means by which people can come into contact with the gospel and the church, but if the HUP grouping becomes an end in itself it is such an insufficient model of church that eventually the gospel integrity of the group will suffer.
A healthy church should be a built in guard against HUP style flattening of the gospel.
Para-church style groupings don’t have that protection.