In a business context, wire transfers have higher fees but go through faster. ACH payments can be 1-day (lower fee) or 3-day delay (free, for us). As other people have commented, ACH is probably less secure than checks, but we've never had any problems with them.

Paypal is not all that trusworthy; they have a history of canceling transactions or tying up funds because they didn't approve of something (including the time they blocked all the transactions for a knitters' sock-kit-of-the-month club, because there couldn't possibly be that many people wanting to knit socks, it must be a front for crime).