Are there any other verbs than 死ぬ whose plain forms end with ぬ? Why are they so rare? Is it because the verb 死ぬ itself has special etymology why it ended up having the ぬ ending?
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As Axioplase has indicated, the verb 死ぬ was originally a n-stem irregular verb (ナ行変格活用動詞). There was only one other such verb, namely 去ぬ. It survives in modern standard Japanese in derived forms such as 古 （いにしえ, from the stem of 去ぬ + the stem of the past tense auxiliary き + the particle へ). It is also thought that the noun 西 is derived from 去ぬ. (The main evidence for this, as I understand it, are Ryūkyū languages in which /nisi/ means north instead of west, indicating a migration from the mainland spreading southwards into the Ryūkyū islands and eastward into Honshū.)
There are also auxiliary verbs which end in -ぬ, the most well known of which is the negative verb. It survives in modern Japanese as the -ん in -ません. (-ず is another form of this auxiliary.) The other one, which does not survive into modern Japanese, is the perfect auxiliary -ぬ, also derived from 去ぬ.
I think that 去ぬ/往ぬ (いぬ) is the only other such verb, and is not standard Japanese. It survived in dialects only, according to http://ja.wikipedia.org/wiki/ナ行変格活用