Hydrogen bonds are important. There, that should be an sweepingly obvious enough statement to get things started. But they really are - hydrogen bonding accounts for the weird properties of water, for one thing, and it's those weird properties that are keeping us alive. And leaving out the water (a mighty big step), internal hydrogen bonding is still absolutely essential to the structure of large biological molecules - proteins, complex carbohydrates, DNA and RNA, and so on.
But we don't understand hydrogen bonds all that well, dang it all. It's not like we're totally ignorant of them, for sure, but there are a lot of important things that we don't have a good handle on. One of these may just have been illustrated by this paper in Nature Structural and Molecular Biology by a group from Scripps. They've been working on understanding the fact that all hydrogen bonds are not created equal. By carefully going through a lot of protein mutants, they have evidence for the idea that H-bonds that form in polar environments are weaker than ones that form in nonpolar ones.
That makes sense, on the face of it. One way to think of it is that a hydrogen bond in a locally hydrophobic area is the only game in town, and counts for more. But this work claims that such bonds can be worth as much as 1.2 kcal/mole more than the wimpier ones, which is rather a lot. Those kinds of energy differences could add up very quickly when you're trying to understand why a protein folds up the way it does, or why one small molecule binds more tightly than another one.
Do we take such things into account when we're trying to compute these energies? Generally speaking, no, we do not - well, not yet. If these folks are right, though, we'd better start.
Update: note that the paper itself doesn't suggest that this is a new idea - they reference work going back to 1963 (!) on the topic. What they're trying to do is put more real numbers into the mix. And that's what my last paragraph above is trying to state (and perhaps overstate): it's difficult to account for these thing computationally, since they vary so widely, and since we don't have that good a computational handle on hydrogen bonds in general. The more real world data that can be fed back into the models, the better.