Getting from Venice to Prague - is there a best way?

Best way schedule wise, or best way cost wise? For schedules, see the German Rail query page.

Fly...

Skyeurope has cheap flights.

When considering "cheap flights", make sure you consider the time it takes to get to and from the remote (eg Treviso) airports used by these airlines as well as the time and hassle of checkin, security, boarding, etc, as well as the cost of getting to and from the airports to downtown. Sky Europe also adds €10 per checked bag (if booked online, more is not), €4 per ticket (person) for payment fee (supposedly for CC usage) and €5-€10 for your seat.

The shortest train journey from Venice to Prague is almost 13 hours...the longest (an overnight train) is 19 hours. I'd fly. Check whichbudget.com and flylc.com for discount airlines making that run (with the aforementioned provisos about flying out of Venice "Treviso" as opposed to Venice Marco Polo.)