another site i've come to love while arranging travel plans for interviews this year is
www.farecast.com
it's kinda like the other flight aggregators (orbitz, hotwire) with the exception that it also includes a heck of a lot of historical pricing information and gives you an estimate of whether the price will change between today and say, the next few days. Managed to save a few hundred bucks "timing" the market.
also helpful in that if you tell it to limit flights to say those that arrive no later than 4pm on a given day it only shows you itineraries that meet that criteria (for some stupid reason, maybe issues on my part, some of the other sites would still show me flights outside of my time preferences)
...
budget as much as you are comfortable devoting to interviews. People in my class picked a wide range of numbers (one guy earmarked 10k in loans for it, saved the cash over like 3 years). Start saving NOW. Interviews are a stressful time, and sometimes having more cash around than you really need can decrease the stress when making last minute travel plans.
A few places gave me interviews with about 1.5 weeks notice back in December when they had cancellations. One place was definitely a surprise (didn't expect to get an interview from there, hell i was honored they even spoke to me lol) and i leaped at the opportunity to go. Having the cash saved up really helped because i was able to book tickets/hotel with the shorter notice and less stress had I not had a bit of an emergency fund saved up.
My advice would be to keep money stashed away for maybe 2 "surprise" interviews. Enough for plane tickets, hotel, miscellaneous. Hotel and misc you can kinda control costs for but keep 300-400 on hand for last minute plane tickets because last minute can mean either very cheap or very expensive tickets depending on city. And definitely look into Amtrak as others have mentioned.