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We have some interesting examples such as Mercury's perihelion

The planet Mercury is especially susceptible to Jupiter's influence because of a small celestial coincidence: Mercury's perihelion, the point where it gets closest to the sun, moves around at a rate of about 1.5 degrees every 1000 years, and Jupiter's perihelion moves around only a little slower. One day, the two may fall into sync, at which time Jupiter's constant gravitational tugs could accumulate and pull Mercury off course. This could eject it from the Solar System altogether1 or send it on a collision course with Venus or Earth.[10]

And also the alignment of Jupiter and Saturn

Yes. When Jupiter and Saturn align, Jupiter's plasma shadow may disrupt magnetospheric activity at Saturn. Jupiter's 1-billion-km plasma shadow (magnetotail) is the largest structure within the Solar System. When Jupiter and Saturn align, Jupiter's plasma shadow can envelop Saturn. Based on Voyager 1 observations, it is plausible - but not proven - that the reduction in solar wind pressure reduces magnetospheric activity around Saturn. This is like drafting an upwind cyclist. http://www.solarviews.com/eng/vg...

But are there any other interesting effects that could be created by other planetary orbit alignments? Especially in exoplantary systems?

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