Malon is a biblical word, originally meaning "lodging place" or more specifically "inn." It derives from the root לון, meaning "to lodge, pass the night." Klein points out that the formation of malon is similar to makom מקום - "place", which derives from the root קום - "to stand".
Klein also mentions that the ultimate origin of לון is probably denominated from layl ליל - "night". (The more common form today, layla - לילה is an extended form of layl.)
There is also an unrelated homonymic root, לון - "to murmur." This is the root of the noun teluna תלונה - "complaint" and the verb התלונן - "he grumbled, complained." Klein writes that it might be cognate with the Arabic lama - "he blamed."
One interesting misunderstanding involving the root לון is related to the upcoming Pesach holiday. There is a requirement, as discussed here, that:
Water to be used in matzah baking must be left to stand overnight (to ensure that it is allowed to cool). This water is then referred to as mayim shelanu (water which has “slept”).
Cool water in matza making is important so as not to hasten the leavening process. The Talmud (Pesachim 42a) after discussing this law, tells the following story:
Rav Mattana taught this halakha in Paphunya. On the next day, the eve of Passover, everyone brought their jugs to him and said to him: Give us water. They misunderstood his expression mayim shelanu, water that rested, as the near homonym mayim shelanu, our water, i.e., water that belongs to the Sage, and they therefore came to take water from his house. He said to them: I say and meant: Water that rested [devitu] in the house overnight.
While the gemara presents this as a curious, and perhaps humorous, anecdote, there are still groups today (as far as I know Hassidic, but maybe there are others) who make sure to use water that they collected themselves for their matza baking. A strange custom perhaps, but it seems that this is the holiday of interesting customs. In fact I know many people whose primary custom is to go to a malon...