Personally, I’ve found Prague to be quite inexpensive to fly into, and I use it as a jumping off point on my little excursions. Has anyone experienced the difference in pricing with other European airports? What place have you found to be the least pricy?
I’m quite flexible, I don’t mind spending time on a train to get to the region I am travelling to if its far from where I fly into.
I don’t know if it’s any help to you, but Ryanair fly all over Europe, mostly using the cheapest airports to save on tax etc. If you have a look at their website http://www.ryanair.com, you’ll be able to see list of the airports they fly to.
These can be 100km or more from the major city they claim to serve, but there is often a bus service. The flights may not be any good to you, but you’ll be able to see some cheap airports to head for.
Disclaimer - not all the airports on there are necessarily cheap.
Any airport can be the cheapest or the most expensive to fly into, it all depends on where you’re coming from and when you want to travel. Simple as that. Give us more specifics, and we might be able to help! 
I’ll be travelling from mid december to mid january. Flying out of San Francisco (SFO) or Monterey (MRY). The benefit to flying out of Monterey is that the airport is literally right behind my house, so I’m willing to spend a few extra bucks for the convenience.
Whenever I fly from DC back home (Netherlands) I fly to Brussels…a) it’s closer to my home than Schiphol (amsterdam) and b) on average about $100 cheaper.
I second RyanAir - haven’t used it myself yet but a friend of mine has family now living al over Europe (Rome, Paris) and he swears by flying to Brussels and then onto RyanAir
But RyanAir is regional only, I can’t fly that line from the US, right?
Right now I usually connect to Prague at Frankfurt. I suppose I could try doing the last leg on RyanAir. Is that feasible?
Ryanair don’t fly to Prague, but other low-cost airlines do. Look at www.whichbudget.com for a comprehensive list of them. However, planning onward connections through cheap airlines isn’t something I’d recommend unless you know the places your dealing with, because it’s easy to suddenly discover an extra cost you hadn’t factored.
I’d strongly suspect that, if your destination isn’t a crucial part of the general plan, that your best bet is keep checking on Expedia etc. and airline sites, between now and mid-October, for cheap deals direct from SFO to London, Paris, Frankfurt, Milan, and so on. Check every couple of days, and you’ll quickly get a feel for ‘typical’ prices. (For example, a sample request on Virgin’s site offered a fully-inclusive $628 for November flights, which strikes me as reasonable but beatable.)
If there was a sure-fire way of getting the cheapest flight possible, we’d all know about it by now.
We do. Join the military.