The Reverso dictionary lists Joghurt as either masculine or neuter. Duden lists it as masculine, feminine, or neuter.
Generally, is there a distinction between using the different genders in such cases? Is there a way to tell which gender is more commonly used?
It depends. In case of Jogurt, there's no difference at all. It's the same thing. Dictionaries provide a single entry with all three genders. Wiktionary even adds some hints:
In Deutschland ist der männliche Artikel am gebräuchlichsten; der sächliche ist eher selten. In der Schweiz und in Österreich wird der sächliche Artikel vornehmlich verwendet, wobei in Ostösterreich - und hier insbesondere der Gegend um Wien - auch noch selten umgangssprachlich der weibliche Artikel verwendet wird
Other words are different. Note, that a different gender is not the reason for a change in meaning. "Der Ball" has two meanings, although both are masculine (round object or dancing party).
Dictionaries provide separate entries if there are different 'versions' of that word. There are words in English, too. For instance, lead (1, 2).
Not exactly. Sometimes dictionaries adds some hints (see Jogurt above). If there's no hint, you can't tell.
Speaking of Ball (still no change in gender), you can bet that people usually talk of that round object rather than a dancing event.
Speaking of See, I'd guess that people usually mean a lake, but well, I go bathing in a lake quite regularly and travel once a year to the sea. Ask people who live at the sea and you may get a different opinion.
There is no way to tell for sure ... some few nouns as "See" do change meaning, but that would be mentioned in the dictionary anyway. You could do a research for regional accents, but if you can, go out and ask people directly. It's a mothertongue thing, and as far as I know, there is no standard rule to find out which one is Hochdeutsch. However, duden.de lists the most common usages, as for "Joghurt" http://www.duden.de/rechtschreibung/Joghurt See "Grammatik" at the bottom of the page. (Which you probably already did. But you won't find much more information outside of linguistic papers ;) )
Yes, certain nouns can be used with two or even all three genders;
der/die/das Joghurt, der/das Teller, die/das Email usw.
Linguistically, they are not particularly interesting. Much more interesting are words that change their meaning, depending on the article used ...
der Tor (fool) vs. das Tor (gate); der Band (volume) vs. das Band (ribbon) vs. die Band (band, as in musical group); der/das Kiefer (jaw) vs. die Kiefer (pine); die Steuer (taxes) vs. das Steuer (rudder)
... or homonyms that have the same article in singular but a different one in plural:
singular: die Bank, plural: 1. die Banken (financial institutions), 2. die Bänke (benches)
singular: der Strauß, plural: 1. die Sträuße (bunches of flowers), 2. die Strauße (ostriches)
Some words I know so far:
Das Plastik = the plastic (material)
Die Plastik = the sculpture
Die Leiter = the ladder
Der Leiter = head/manager/director/leader
"Anerkenntnis" is another case of two genders and usages. There seems to be no rule of thumb for distinctive meanings attributed to any gender here.
Der / die See have different meanings. Most nouns don't. The genders of those words varies regionally. It would be strange if you would mix usages of different regions.
Examples:
In my humble opinion, Joghurt to be treated as an uncountable mass, like Mus. If referring to a serving of joghurt or particular kinds (as for the sands), you might use an article, and der Joghurt might well derive from der Joghurt-Becher, which is quite idiomatic, and ein Becher Joghurt*, equivalent to "Ich trinke ein (Glas) Wasser", though nobody eats a "Joghurt-Becher"; likewise die Schale Joghurt or das Glas/Schälchen Joghurt, or whatever else. The plural -s carries over, but sounds just a little weird, "Ich habe 5 Muse gegessen".
Indeed, die and das Mus both exist, but only der Sand. I'd speculate that age of the word plays a role, because many transgender words (what's the correct term again?) are borrowed (apple sauce vs Apfelmus, hence unlikely Germanic; ). Given enough time, a variant might win, and for diverging senses, separate genders might proliferate.
The uncountable distinction might not work for all words, and the substitution heuristic might not be all that is too it. Euphony could play a role, if vowelharmony differs across dialects.
