For those of you who have experience flying out of smaller cities,
what do you recommend?
I'll give you my experience. I fly out of GSP (Greenville-Spartanburg, SC). I use Delta exclusively because I'm in the top tier of their frequent flyer program and because I truly love flying with them (weird to say about an airline, I know). "Published" fare sales come out every Thursday morning, but random 12-24 hour non-published sales can pop up any time and can be highly market specific (for example, I once found deeply discounted fares on a Tuesday evening that lasted only for that evening and applied only to the GSP, CLT, and CAE [Columbia, SC] markets). If I see a reasonable fare, I snag it. Once you get to 120 days before a flight, fares tend to rise and fare sales become highly targeted (often requiring a Tues-Thurs departure/return).
My typical strategy is to check prices morning and evening every day once I have a trip finalized. I just check the Delta website but you can cast a broader net with Kayak. On the Delta website, you can click on the "Flexible Dates" link at the top of the fare result page to see fares for a week around departure/return dates. Sometimes a day or two can make a huge difference in the fare.
I'm willing to pay a bit of a premium to fly out of GSP but have also driven to Atlanta for cheap fares. This year, I've noticed that fares have been significantly higher out of GSP and ATL than in years past (like $400-$600 higher). My theory is that since there are no discount trans-Atlantic carriers in the region, Delta (and the other US airlines) are pushing up fares here to counter the lower fares in other markets with discount trans-Atlantic carriers.
So... for a trip this past May, I had the option of flying to Berlin for $800 r/t out of JFK or $1600 out of GSP/ATL. I went for the former. On the day of the Berlin flight (5:30 pm departure from JFK), I flew the early-morning GSP to LGA flight (paid $200 for it), arrived at LGA at something like 8 am, went into the city to visit with my travel companion's sister, and then headed out to JFK. It worked fine. For our return home, we gave ourselves 5 or 6 hours between our arrival at JFK and departure at LGA, caught a cab after arriving at JFK, and waited a really long time to catch our flight home from LGA. I was willing to take the risk because (1) we built a lot of extra time into the schedule between flights if things went wrong, (2) there is a lot of redundancy in Delta's system from GSP to JFK, and (3) Delta overall is so reliable. I'm doing something similar this Saturday for a round-trip flight to Frankfurt ($800 out of JFK vs $1800-$2000 out of GSP/ATL), only this time I'm flying into JFK from GSP via ATL. I'll let you know how it works out this time. :)