I was rooting through the literature, but there is too much work on the topic of detecting loops in RNA and the RNA helices that go with them. Can anyone point to a good review on this topic or even better describe some better performing algorithms?
I frankly don't trust Mfold or RNAfold for finding structure. There are just too many false positives and without experimental verification, it's not reliable. For finding hypothetical local structure, it's great. However to find evolutionary conserved structure MSA methods like what has been used with Rfam are a more suitable way.
Since you asked for Reviews, any of Sean Eddy's Rfam updates are good. I also suggest checking out https://www.mendeley.com/groups/545791/rna-structure/.
But for now, I think Revolutions in RNA Secondary Structure Prediction by David Mathews who developed the Turner rules and Mfold is a good start.