Store Emails going to Spam Folder

Our store emails including the order receipts sometimes end up in the spam folder. Is there any way to ensure that they don't, or is that a common issue?

You say that they sometimes go into the spam filter, when they are not being flagged as spam can you see anything different? In general the exact things that are being filtered out are not always known, catching spam legitimately is a cat and mouse game so the process for detection is always changing. You should make sure that the return address is accurate and comes from the domain that sent the email. Also you may want to try adjusting the subject text in the settings of your admin area.