1. Bodkin must mean "little body." Didn’t Hamlet say something about a “bare bodkin”? He did. But he was talking about taking the “not to be” option, ending his suffering with a bodkin, or dagger. (Origin unknown.)

2. Crapulous sounds cruddy. After all if Bart Simpson uses craptastic to mean the opposite of fantastic, crapulous must be the opposite of fabulous; right? Wrong. It means "characterized by gross excess in drinking or eating" or "hung over." (From Latin crapula, "inebriation," and Greek kraipalē, "drunken headache.")

3. Crepuscular refers not to an oozing skin ailment but to twilight or to creatures active at twilight, like bats, mosquitoes, and vampires. (Mid 17th cent.: from Latin crepusculum, meaning "twilight.")

4. Formication may sound sexy, but it means "an abnormal sensation as of ants creeping over the skin." (From Latin formīcāre, meaning "to crawl like ants.")

5. Funambulist sounds like it should be the driver of an ambulance decorated with happy faces, but it’s actually a tightrope walker. (From Latin fūnambul-us—fūn-is, "rope," plus ambul-āre, "to walk’" plus the -ist suffix, "designating a person who practices some art or method.")

6. Fungible sounds like it describes a squishy, spongy fungus, but it’s a legal term describing goods or money that can replace or be replaced by equivalent items. (From medieval Latin fungibilis; from fungi, meaning "perform, enjoy," with the same sense as fungi vice, "serve in place of." It’s not related to fungus, which is related to sponge.)

7. Noisome doesn’t mean noisy, but stinky or otherwise disagreeable or offensive. (From the obsolete late Middle English word noy, a shortened form of annoy, plus -some, an adjective-forming suffix.)

8. Nugatory sounds creamy and delicious but it means unimportant, of no value or useless; futile. (From Latin nugatorius; from nugari "to trifle"; from nugae, or "jests.")

9. Pulchritude sounds like the ineptness exhibited by a lurching klutz, but it’s a highfalutin word for "beauty." (From Latin pulchritūdō, "beauty" by way of Middle French.)

10. Plethora may sound like an ancient Greek musical instrument, but it means an excess of something. When it entered English in the mid 16th century, it was a medical term for an excess of a bodily fluid, particularly blood. Although modern medicos have given up leech therapy, plethora is still used to mean an excessive volume of blood. (Via late Latin from Greek plēthōrē, and from plēthein, meaning "be full.")

11. Callipygian sounds like a bird with a suntan and a laid-back attitude, but it means "having shapely buttocks." (From Greek kallipūgos, which was used to describe a famous statue of Venus, and from kallos, or "beauty," and pūgē, or "buttocks," plus -ian.)

Sources: Oxford English Dictionary Online, New Oxford American Dictionary (Second Ed.), The American Heritage Dictionary of the English Language (Fifth ed.)