It depends on the setting.
Space opera? I love it, and I love the genre conventions, which mean the aliens are at least vaguely humanoid - otherwise you can't have the obligatory alien princess falling in love with the human hero without bordering on bestiality. If the setting involves cutlasses, ray guns, and giant riding lizards, the aliens (or most of 'em) should be humanoid.
Hard science fiction? The aliens are likely to be that gray-green lichen-looking film covering the rocks over there - and yes, it's a highly intelligent species.
I think this is one of the most challenging things to make "believable" in a hard sci-fi setting. One of the pass-arounds I've used is to postulate a common origin for certain species - many alien races are derived from one ancestor race and represent divergent evolution, for example. Another is to assume a certain level of convergent evolution - perhaps the bilaterally symmetrical body plan is ultimately the most efficient for carbon-based lifeforms on earth-like planets? Right now our sample set is too small to draw any firm conclusions.
There are ways to have humanoid-ish lifeforms in a hard sci-fi setting if you want them - the kzin of Larry Niven's Known Space are no less believable than puppeteers, IMHO. (BTW,
Ymdar, the alien in the
Aliens saga is humanoid and looked like a person in a really well-done latex suit, and it was still cool.)