I think there are many examples. A lot of my personal background is in database systems: off the top of my head, non-consumer oriented startups in that domain include startups that are trying to beat Oracle at transaction-processing (EnterpriseDB, MySQL AB to some extent), and a whole bunch of startups in the data warehousing area (Neteeza, Greenplum, ExtenDB, ParAccel, Datallegro, etc.) In data stream processing / complex event processing, there is StreamBase, Coral8, Apama (although they've been acquired by Progress), etc.). There are lots of hard, enterprise technology problems that haven't been solved very well, and that are ripe for entrepreneurs. There are similar problems in data integration, networking, virtualization, security, storage, DRM, etc.
And that's without even thinking about vertical markets. For example, I think if you sat down in a room with an industry expert in, say, the oil & gas industry and a few smart hackers, you could come up with a way to apply computer science to improve oil and gas prospecting. There are dozens of similar vertical markets, where some smart hackers with a modicum of domain-specific knowledge could really make a pretty significant improvement on the state-of-the-art, IMHO.
The group-think among certain communities on the Internet toward consumer-oriented, Web 2.0, advertising-dependent web startups is really pretty amazing -- I just get terribly bored reading about all the different people building Web 2.0 task management web apps and similar junk. There are lots of other kinds of startups out there -- it's just that YC doesn't focus on funding them, and TechCrunch doesn't cover them, so this particular community of developers never learns about them.