In roughly decreasing order of annoyance:

A varying degree of belief in utilitarianism (ranging from a confused arithmetic altruism to hardcore Benthamism) seems to be often taken for granted, and rarely challenged. The feeling I get when reading posts and comments that assume the above is very similar to what an atheist feels when frequenting a community of religious people. The fix is obvious, though: I should take the time to write a coherent, organised post outlining my issues with that.

A little Singularitarianism, specifically the assumption that self-improving AI = InstantGod®, and that donating to SIAI is the best possible EV for your cash. This isn't a big deal because they tend to be confined to their own threads. (Also, in the thankfully rare instance that someone brings up the Friendly AI Rapture even when it brings nothing to the conversation, I get to have fun righteously snarking at them, and usually get cheap karma too, perhaps from the other non-Singularitarians like me.) But it does make me feel less attached and sympathetic to other LessWrongers.

Of late, there's a lot of concern about what content should be on this site and about how to promote the site and its mentality to the 'muggles'. This kind of puzzles me, because I treat LW as just a place where mostly smart INTJ people hang out and flex their philosophical muscles when they feel like it, and I don't feel particularly interested in missionary work. While I do find it desirable to make more people more rational, I thought everyone here - except for those who get their paycheck from SIAI/FHI, I guess - had better and more efficient purposes to which to dedicate their precious, precious willpower-to-do-stuff-I-don't-enjoy than writing posts they don't really feel like writing. If providing "hardcore" content to LW feels like a chore, then we have a tragedy of the commons situation at hand, and is the site important enough to implement one of the standard workarounds to it?

Eliezer's reduced presence. Other contributors' posts are even more productive and useful than his, but none are quite as enjoyable to read.

Some top contributors regularly get double-digit karma for utterly trivial comments. Can't think of a fix that would be less annoying than the issue.

More Anglo prevalence than I would have expected for a site like this.

No Auto-Pager script for people's histories.