Two verbs I tend to confuse in Spanish are amanecer (to dawn) and amenazar (to threaten). This is something that my Spanish friends can find highly amusing of course, but I have heard of many people having similar problems with certain pairs of words. Everyone has their own mental blocks when learning a language, and you will find your own problem words as you go along.
For me, the solution is to identify the problem words and come up with a way to remember or distinguish them. With my example above, I think of the verb 'to menace' as being similar to 'to threaten', and look for 'menace' with an 'a' in front becoming 'amenazar'.