Here's some suggestions ...
The visa issue has been around in some form or another for at least a decade. As an academic conference organiser, I have seen the UK Border Agency turn down PhD students from the German Supercomputer Centre. After paying €700+. Admittedly, both were Iranian nationals, and on reflection I should have been more careful in obscuring the nature of our get together: mentioning "supercomputers" in a visa reference for an Iranian national was a bit of a red rag to a bull.
Now, on the practicalities of organising conferences. Ideally you'd like to be able to fly in directly to an international airport, hop in a taxi, train or bus and get out at the destination hotel/venue. Since there are a lot of PhD students attending, you need to keep the price down, but you also need the facilities available. For this reason, out-of-season holiday destinations can be quite attractive.
So, in no particular order here are some suggestions for conference venues where visas are less of an issue:
North America: Vancouver, Montreal, Toronto.
Italy: Amalfi Coast (fly in to Naples), Sardinia, Sicily (involves an extra flight).
Greece: Any of the Island (but involves an extra flight)
Belgium: Bruges (easy to get to from Brussels).
Germany: ICE trains make airport connections in Munich dead easy. Rhineland wine-growing regions are only 30km from Frankfurt Airport.
Sweden/Denmark: A bit expensive, but there are often youth hostel type hotels in interesting destinations in the islands and forests.
France: Try working out from Lyon rather than Paris (CdG). North to the Mâconnais, or even the city itself. The area around Marseille can be good.
I'd also think about Romania or Estonia these days.