What's the best way to determine interplanetary launch windows?

[Kasuha]

Yeah, I learned that the hard way last night ("that's what she said"). Seriously though, I used the Alex Moon site to get a departure time, used Precise node to set up my maneuver, and got a ballistic encounter with Duna for just 600m/s (just half of the estimate calculated on Alex Moon). I was psyched. But then the burn took like a half an hour, and it totally threw off the maneuver. Is there any way to avoid this, besides adding more engines? On that note, what's generally considered to be the minimum TWR for interplanetary burns?

If your maneuver required significantly less dv than what the planner told you, then you probably did not enter your orbital altitude correctly into the planner.

There are two ways to correct for inaccuracies caused by long burns.

1/ divide the burn into two or more. Set up a maneuver, burn along it but when you get too far from the maneuver, stop burning, delete the maneuver, and set up another one. Do not put your apoapsis too high or you might miss your launch window - intermediate orbits should not go higher than about to Mun.

2/ when you're already on exit trajectory and you see you're starting to diverge, disregard the maneuver marker and instead switch to map view and watch the point where you should exit the Kerbin SOI according to your maneuver, compared to where the appropriate point is on your trajectory. Steer your burn so you get the two to overlap but watch out - you need to match them not only in space but also in time. When you put your mouse over the marker, it displays in how long you're supposed to pass that point. You need to make the two timestamps match as well. Notice you will be burning in very different directions than what the maneuver marker tells you.

[MerlinsMaster]

If your maneuver required significantly less dv than what the planner told you, then you probably did not enter your orbital altitude correctly into the planner.

You're right. That particular burn was from a higher orbit. I completely didn't think about that.

intermediate orbits should not go higher than about to Mun.

What's an intermediate orbit? I usually never get an escape trajectory until it's out past Mimnus.

Also, on a loosely related note, is there a way to fine tune my destination periapsis before I get to my destination's SOI? For example, on my escape burn, I got an encounter with Duna, but the lowest I could get the Pe down to was 30000km. Is there any way I can get it lower before I get there?

[cantab]

What's an intermediate orbit? I usually never get an escape trajectory until it's out past Mimnus.

In this case it's referring to a highly elliptical orbit with periapsis low (say 70 km) and apoapsis up high somewhere. It's what you'll get if you have to do your ejection burn in more than one go. You can burn something like 800 m/s, orbit round, then burn the rest. Watch out for the Mun!

Also, on a loosely related note, is there a way to fine tune my destination periapsis before I get to my destination's SOI? For example, on my escape burn, I got an encounter with Duna, but the lowest I could get the Pe down to was 30000km. Is there any way I can get it lower before I get there?

Easiest way is to correct on entering Duna's SOI with a normal+radial burn, a more efficient way is to make a mid-course correction about halfway along your transfer.