For some problems, it may be nice to have a generative model as offered by RBMS (although Rifai et al. published a sampling method for contractive auto-encoders recently: http://icml.cc/2012/papers/910.pdf). I feel like with RBMs, you can design models which incorporate prior knowledge more "easily" (you may end up with pretty complex models...), e.g. the conditional RBM, the mean-covariance RBM or the spike & slab RBM. Additionally, there's the deep boltzmann machine that consists of multiple layers that are jointly trained in an RBM-like fashion.
Auto-encoders are straightforward to understand and implement. With contractive terms or denoising, the are powerful feature extractors as well.
But as you already noted, if you "just" want to have a good classifier, I think it pretty much boils down to personal preference since you're going to spend some effort on making these techniques work well on your problem anyway.
We could also pipe the raw data through an RBM and then slap a SVM or some other classifier on top.
After all, a deep belief network starts with an RBM for unsupervised pre-training, but the finetuning stage that follows just treats the network as a standard MLP using backprop.
Also, you can use an autoencoder instead of an RBM, which I think are getting better results these days? And there are better regularization techniques for backprop now--weight decay, momentum, L1/L2 regularization, dropout, probably more that I'm leaving out.
The pre-training (RBM or autoencoder) helps to not get stuck in local minimas, but there's also interesting research that suggests you're not even getting stuck in local minima so much as you're getting stuck in these low slope, high curvature corridors that gradient descent is blind to, so people are looking into second order methods that can take curvature into account so you can take big steps through these canyons and smaller steps when things are a bit steeper. Or something like that :-)
All that being said, anyone care to weigh in on the pros/cons of RBMs vs something like a contractive autoencoder? No such thing as a free lunch, so what are the key selling points of RBMs at this point? I keep seeing them pop up, but afaik, they don't provide a particular advantage over autoencoder variants.
Great article though, I'm really glad to see more and more people getting interested in neural networks, they've come a long way and people are just starting to wake up to that.