There are no clear rules on when to use the voltooid tegenwoordige tijd (hebben/zijn + ge..), but I would say that in most cases, you want to use this tense.
You sentence should be: "Ben je gisteren vergeten te Skypen?". We use Skypen as a verb in The Netherlands. "Heb je .." is also correct, but I don't hear this often.
"Vergat je gisteren te Skypen?" (onvoltooid verleden tijd) is gramatically correct, but makes less sense.
The onvoltooid verleden tijd ("vergat") is used mostly for storytelling. "Ik vergat te Skypen, en toen...".