Taken from the first post:
Tl;Dr: I translated them from the Elder Futhark runic language, and they each say something strange.
NOTE: These translations were of my own work and other people who filled in the blanks or corrected me on things. I do not claim entire credit for it.
The runes on the bee one translate to GIANT/THOR-HAIL-NEED
The runes on the butterfly one translate to JOY-ICE-SORROW
The runes on the dragonfly one translate to NEED-HORSE-LAKE.
The runes on the moth one translate to DAY-NEED.
The runes on the torchbug one translate to YEW TREE-HORSE-HAIL-NEED.
There have been many theories created while this thread has existed, most notable of which are mentioned below.
EDIT: This has blown up from runes on bug jars to theories about a religious Altmer trial to wipe mankind off of the plane of existence and from Tamriel. There's two likely theories here: the first one should be easy to find, it's the top comment, and the second one expands upon the Weynon stones, for which I will include a link: http://www.reddit.com/r/skyrim/comments/nklj2/you_know_those_runes_on_the_lids_of_the_bug_jars/c39wpky
EDIT:EDIT: Upon recent investigation, I'm not sure if all of my translations were completely right. Either way, this translation of the runes has led to the discovery of the Transmutation circle between the five cities, so this could still mean something. A more accurate translation and meaning of the sets of runes: http://www.reddit.com/r/skyrim/comments/nklj2/you_know_those_runes_on_the_lids_of_the_bug_jars/c39z2gn
I'm feeling this is required for the lazy, but here's a Tl;dr of the two prime conspiracy theories.
Someone noticed the connection between the five cities Morthal, Whiterun, Winterhold, Dawnstar, and Windhelm, and realized they formed a Pentagon. He also noticed three dragon "sanctuaries" or whatever you may call them, Mzinchaleft, and the Tower Stone formed a smaller pentagon within it, making a transmutation circle. In the general area of the middle of the circle, there is a shrine to Talos with a circle of stones around it. His theory was that if you placed the bugs on their respective cities (see post for relation between bugs and cities), committed genocide in those ctities, kill the dragons at the dragon areas and the one that Mzinchaleft leads to, activate the tower stone, and wait for the "Promised Day".
The second one expands upon the Weynon stones. The guy figured out that the Thalmor are trying to erase mankind from existence, and the things that are stopping them are the eight towers:
all of which were destroyed or deactivated. The most significant and only remaining one are the Brass Tower and Snow-Throat, or the Throat of the World. The Brass Tower was cast out of time. The tower may have a spiritual connection with Numidium, the brass god, and the disappearance of the tower and therefore Numidium may tie in with the disappearance of the Dwemer. Snow Throat is the only active one. Each of these towers have stones which bind them to Nirn, and the theorist concluded that the Weynon Stones bound Snow Throat. This is why the Thalmor have been waging war on Skyrim; so they can destroy Snow Throat or the Weynon Stones, either way destroying the last tower and wiping mankind from existence.
Something else has come up; Under the Weynon Stones in Blackreach is the Hall of Ruminations!"
There are posts below it in the topic, but that is the bulk of the idea. Pretty cool stuff!