Establish a strong social script regarding instances where words should be taken denotatively, e.g. Crocker's rules. I don't think any other obvious strategies work. Hidden connotations exist whether you want them to or not.

(non-existent)

This is the wrong attitude about how communication works. What matters is not what you intended to communicate but what actually gets communicated. The person you're communicating with is performing a Bayesian update on the words that are coming out of your mouth to figure out what's actually going on, and it's your job to provide the Bayesian evidence that actually corresponds to the update you want.

Become more status conscious. You are most likely inadvertently saying things that sound like status moves, which prompts others to not take what you say at face value. I haven't figured out how to fix this completely, but I have gotten better at noticing it and sometimes preempting it.

I wish I could upvote this question more. People assuming that I meant more than exactly what I said drives me up the wall, and I don't know how to deal with it either. (but Qiaochu's response below is good)

The most common failure mode I've experienced is the assumption that believing equals endorsing. One of the gratifying aspects of participating here is not having to deal with that; pretty much everyone on LW is inoculated.