Just a thought, but I think that this could have been used if the writers had thought about it:

Jane got close to Red John, VERY close, in the episode where Red John saves him from the copycat killers.  So close, that I'm sure Jane probably had a perfect opportunity to get a whiff of what Red John smelled like!!

This might not be a big clue to any normal person, but we know that Patrick has a very keen sense of smell, and smell is the most powerful sense in terms of memory...So, one might think, if Patrick got THAT close to Red John, he might be able to recognize the smell and connect it to one of the 7 suspects!!

Obviously there are some holes in this theory:
-The room could have covered up his scent
-He could wear cologne in his daily life to cover up his real scent
-Being in that costume could have made him smell differently
etc...

But I would think that if Patrick Jane got THAT close to Red John...(assuming it really was Red John who saved him)...I would think that he could have gotten some sort of an idea for who he is.

Other things he could have possibly picked up:
-breathing patterns
-if he got a good enough look at him (maybe he didn't) he could have got a good sense of his height/weight
-his voice/way he talks:  he obviously didn't talk normally, but even when you use a different voice, there are usually still some things that stick out

What do you guys think?