Although my problem is specifically related to the yahoo online dictionary, I imagine somebody using another dictionary might have come across the same problem before me.

So when I look up a word, I often get a list of multiple ways to write the word out in kanji, i.e. looking up あう gives me:
あ・う〔あふ〕【会う／遭う／▽遇う／×逢う】
If nothing is written next to the numbered definitions below, I just default to using the first (and most common) way to write the word, i.e. 会う in the example above. Sometimes the dictionary also lists which kanji to use for a particular definition, i.e.
２ （遭う・遇う）好ましくないことに出あう。「事故に―・う」「強い反対に―・う」
In which case I'd pick 遭う (presumably the most common of the two). This is all fine.

The problem I have comes to which kanji representation to pick when they write like this:
かか・る【掛（か）る／懸（か）る／係る】
(...)
４
①（「架かる」とも書く）物が一方から他方へまたぐように渡される。「橋が―・る」
(...)
If I were looking up this particular definition from かかる, how should I write it in my SRS entry? Would it be more proper to choose 架かる or should I read 「架かる」とも書く more as an implicit "well, some might also write it like this, but you shouldn't bother doing so yourself." and choose 掛かる in my SRS entry?

I'm even more confused in the following situation:
まち【町／街】
(...)
２ （「街」とも書く）商店の並ぶにぎやかな場所。市街。「―をぶらつく」
(...)
Where they write 「街」とも書く when it has already been stated that both 町 and 街 are possible representations at the top. Does this mean that 街 is to be preferred over 町 in this case even though they are both correct, unlike if they had simply written
２ （街）商店の並ぶにぎやかな場所。市街。「―をぶらつく」
in which case that should be interpreted as only 街 would have been allowed?

Yahoo might have somewhat clarified this themselves here:
http://dic.yahoo.co.jp/guide/jj/jj3_1.html
under point number five, but my Japanese is not at the level where I can fully understand the explanation yet.
Sorry for the long question, but I hope someone can help me out as I've been wondering about this for quite a while, but couldn't find any explanations in English.

Unfortunately this is a tough question that can only be really solved on a case-by-case basis, looking at actual usage. As far as I know, there is no resource that gives clear guidelines for kanji choice that's based on the way the kanji are actually used rather than prescriptive rules.

I would put it in your SRS the way you saw it written wherever you got the word from. That should be safe in most cases.

Thanks for the answer yudantaiteki.

Usually I would put it in my SRS the way I saw it written if it was written in kanji, but the problem is that as my Japanese is still very basic (I'd say a bit short of JLPT5), most of the material I have access to tends to be written using LOTS of kanas, and I prefer to enter the words into my SRS in their kanji forms right off the bat to reap the benefits of having completed RtK, and avoid having to relearn words in their kanji forms later, which means I am usually on my own when it comes to finding the kanjis (which is what I use the dictionary for, hence my original question).

Can I do anything to ascertain myself to some degree about which I should use on a case-by-case basis given that my Japanese intuition and experience is next to non-existent at present? My first idea would be to google it and see the amount of hits for each way of writing the word, but the problem is, that seeing as I am looking for kanji uses for sub-definitions of the same word, the hits related to each way of writing the word doesn't necessarily correspond to which form is primarily used for that particular sub-definition.

When I stumble upon words with massive, or otherwise confusing definitions I tend to simply not add it to my SRS and learn it on the side instead. In cases such as the ones you stated I would google it; "掛かる 懸かる　係る　架かる" and "会う　遭う　遇う　逢う" in this case. Usually you're not the first person who's had a problem with that word, so there are almost certainly threads about it around the internet (知恵袋 etc) where people explain how to use the words.

The possible downside to this of course is if your Japanese isn't quite up to the level where you can take full advantage of it. Nevertheless I think it's a good habit to get into, and it should get easier by time as you read more and more explanations.

First, don't worry too much about it. The first one is almost always going to be the most common and generic one and perfectly acceptable. The others variants are either used to add a special nuance or simply use non-joyo characters or readings (▽ = non-standard reading ×=non-joyo character).

When there is a strong difference in meaning, there are usually going to be multiple dictionary entries (notice how on yahoo 会う and 合う are not on the same entry, those two should not be confused).

Your IME might help you, at least on Windows, I don't know if other systems have it too. When converting to kanji and there are multiple choice there are often little notes that provide an explanation of what the nuance is and an example sentence.

Don't worry about it. If you're learning the words in kana, put them in your SRS in kana and learn the kanji later. Otherwise get some other book/resource that already has them in kanji.