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Apparently, the MD-88 has a strake on both engines: enter image description here Source: Airliners.net
If I'm not wrong, the engine strake attaches the airflow at high angles of attack on the wing. But in this case the engine is behind the wing. So what is the purpose of this little fin? Is it a strake or something else?

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    $\begingroup$ Flow separation always produces considerable drag. So even though it is behind the wing, and would not affect lift, flow separation is still undesirable here. $\endgroup$ – Jan Hudec Apr 9 '16 at 16:36
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They are indeed strakes which serve to reduce flow separation on the lower rear engine fairing by creating a vortex which will mix the outer, faster flow with the slowed down boundary layer on the lower rear part of the fairing. You will notice that the nacelle is mounted at an angle of 3 degrees to the fuselage: This is to position the intake and nacelle in line with local airflow, which is pointing slightly downwards at the rear fuselage due to the wing's downwash. The exhaust is again pointing directly back, so the thrust will be aligned with the lengthwise axis of the fuselage and will not produce pitch moment variations when thrust is changed. In combination with the nacelle incidence this produces a more pronounced curvature on the lower side of the nacelle, which in turn is more prone to flow separation.

You could as well place a row of vortex generators on the bottom of the fairing, but the strake will produce less drag when downwash is low and its service is not needed. With higher downwash, the strake will produce a stronger vortex, just when it is needed most.

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