Underscore, when used as a verb, also means to emphasize or stress--a figurative underlining in (non-written) communication; to give extra weight to, as in His tone underscored the importance of the event, or The fact that she was moving so slowly underscored her reluctance.
Merriam Webster reminds us that underscore can also mean ‘to provide (action on film) with accompanying music.’
The Wordsmyth English Dictionary-Thesaurus elaborates. Underscore can mean: accent,
On E2, underscored words can be hardlinks or pipelinks, or they can simply be underlined words. Use brackets [ ] to create links; use HTML tags < u > and < /u > to underline.
Under Words of advice for young noders it says to never ever use a link for emphasis; use the underline. As heyoka points out, however, strictly speaking, with HTML, one should use the < em > tag for emphasis...
...or < i > for italics.