Don't know much about this domain... here are some links:
- RNAfold The standard in RNA folding, only one sequence
- Mfold Good old traditional RNA tool, only one sequence
- PFold can fold multiple alignments
- RNAz like RNAfold, strange SVM, but can be applied to the whole genome
- RNAz predictions conserved in human/mouse/rat/dog/chicken This is a simple bed-file that you can view on UCSC, overlap with anything, very nice data
- QFold similar to RNAz, slower?
- Mirscan folding and miRNA prediction