I've been using a basic 4-1-4-1 counter. Was having pretty decent success with it with Hull City. I was already toying with it but Cleon's Counterattacking thread on SI gave me some more insight.
Mentality - Counter
Team Shape - Flexible or Rigid (Rigid will restrict the overall creativity in the side more so I base it on the players I have)
GK-D
FB-S
CD-D
CD-D
FB-S
AM
WM-S
B2B-S
CM-D
WM-S
DLP-S or DF-S
No TIs.
I tweak accordingly. If I have a very attacking FB, I might go FB-A. If I have a more attacking winger, I might go W-S. I try to stay away from too many attacking roles, because I want the primary intent to be maintaining shape and defensive structure. The CM roles can be adapted as required - CM-S or possible even CM-A against a side that is going to defend more, etc. With WMs, its easy to tweak them with PIs, which makes them quite versatile.
TIs are added as needed as tweaks. A deeper defensive line is helpful if I have really slow defenders or need to draw the opposition out. Retain Possession is helpful for killing off a game. When a counter-attack possibility is triggered, that event overrides most settings anyway so there really isn't need to try to find TIs to help it. The TIs are more about how we play defensively and with the ball in a normal, non-counter but still attacking situation.