You could use these as questions and they would all be understood by an English speaker. However, it would be best to switch the word order. Question words in English usually come at the beginning of the sentence. Can we speak English on Skype? Can we have a conversation over Skype? Can we speak English through Skype? Can we speak English with Skype?

You could use these as questions and they would all be understood by an English speaker. However, it would be best to switch the word order. Question words in English usually come at the beginning of the sentence. Can we speak English on Skype? Can we have a conversation over Skype? Can we speak English through Skype? Can we speak English with Skype?

All correct, it's just a matter of choice and perhaps context of the conversation. Sometimes in English you can have many 'Best s' sentences for the same situation.