Yea, Set Variable wins hands down.
The second would be a toss-up between For-Loops and If/Then/Else...
Perhaps somewhere in the top 10 should be Unit - Create Unit <etc> for all my spell triggers :P Oh, and not to forget Trigger - Run <trigger> & Trigger - On/Off.
Apart from command lines such as set variable, loop, if/then/else mine are:[list=1][*]Wait[*]Set unit life to value[*]Get units in range of location[/list=1]
I'm JASS scriptwriter so I don't use GUI triggers :) As for fafourite functions - I have no one because I often use different functions for my scripts.