$r is just a very undescriptive (and therefore *bad*) alias for $rand(). Perhaps if it's not going to be removed anytime soon it should be noted under $rand() for those who see it in a script and wonder what it is, but I don't think it's use should be encouraged.
Other undocumented commands:
$nickmode, $remote, /setlayer (now that the bugs are gone), /registration
Other undocumented alias commands:
/leave (/part), /quote (/raw), /wallchops (/onotice)
Also $ok, $cancel, $yes, $no, $true, and $false are all unindexed.
$mididir is still documented under File and Directory Identifiers despite being deprecated.
