As already stated, you can't do comments. However, it is possible to effectively disable commands. Since the Apex executes top to bottom, you can just add the new code at the end. The only exception would be Defer and Min Time that always execute last regardless of position. So for example:
[Heater]
If Temp < 78.0 Then ON
If Temp > 80.0 Then OFF
If Temp < 76.0 Then ON
If Temp > 78.0 Then OFF
The code in blue is superceded by the later code. However, I do think comments would be useful.
Todd