This is how I do it. Essentially by using Bash's backtick command substitution one can place these comments anywhere along a long command line even if it is split across lines. I have put the echo command in front of your example so that you can execute the example and see how it works:
echo CommandName InputFiles `#1st comment`
--option1 arg1 `#2nd comment`
--option2 arg2 `#3rd comment`
Another example where you can put multiple comments at different points on one line:
some_cmd --opt1 `#1st comment` --opt2 `#2nd comment` --opt3 `#3rd comment`
与恶龙缠斗过久,自身亦成为恶龙;凝视深渊过久,深渊将回以凝视…