Depends. There are a lot of forms that have evolved very similarly in completely different forms. Wings have arisen in at least three different lineages (insects, mammals, birds) that don't share wing-bearing ancestry. While they're formed differently (insects have a different body plan; while birds and mammals are both tetrapods, bird wings are adapted arms while bat wings are adapted hands), they are all at least somewhat similar mechanically. The eye has evolved separately as well.
And there are more general forms that are just physiologically inevitable, like heads (very few things can move equally in all directions; this gives you a forward. Once you have a forward, it works better to put sensory organs up front, and that's why heads are pretty common).
So, really, if you think about what a sentient life form from another planet would look like, it's most likely going to have a head with eyes (and other sensory organs), and may well have limbs adapted for manipulation instead of locomotion -- and may have those secondary to evolving an upright stance.
So all in all, I don't think seeing alien races that have recognizable physiologies is that unbelievable; the thing that most sci-fi gets wrong, to me at least, is that I don't think there's any good reason to expect any similarities of *digestion*, as that's a matter of the particular chemistry of each environment...