One that I always find funny now that we've seen so much of the show was when he and Happy were off to get the airport's old data system in the pilot and he says "tell the waitress I'll be right back." Because like...there is zero Toby/Paige flirting or implications at all through every single other episode but in the pilot Toby just has that moment where he's like "oh hope she doesn't miss me!"
And I believe that was ad-libbed too, because in the commentary for the pilot they mentioned occasionally ad-libbing and Eddie asked "did 'tell the waitress I'll be right back' make it in?"