What software is available to convert interlaced 3D video to a RealD (side-by-side) format? StereoMovieMaker splits it up, and doesn't carry over the audio.

StereoMovie Maker does support audio for sure. Maybe you are doing something wrong (I haven't used it in a while so I don't recall the steps).

The video is a VOB source (mpeg-2 encoding, AC-3 audio), and it's stated on the site StereoMovieMaker doesn't support it. Also, other than Roxio, what's the best 3D DVD burner software?

Did you see this:

And I have ffmpeg.exe in the folder, no dice. It just doesn't support AC-3 or Mpeg-2 audio over here.

You can do conversions between 3D formats with MPlayer/Mencoder, but it's a command line tool so not really easy to use. In this thread you can find examples for converting between interlaced and side-by-side (search for "interlaced to left/right") : viewtopic.php?f=27&t=4521

AviSynth should do the trick too... by using DGMPGDec for reading/decoding the VOB file(s) (and demuxing all audio streams at the same time), SeparateFields for separating odd and even fields into different frames, EEDI2 (or a simple Resize Filter) for height doubling, Select for separating even and odd frame numbers (= separating left and right view, produced by SeparateFields) and StackHorizontal for outputting left an right view side by side.

The typical AviSynth script (without EEDI2 <= cause it's very slow, but delivers great quality) for converting an interlaced 3D clip into half side-by-side should look like this:

This script can be treated like a video file, for feeding most video applications or encoders with. It may be necessary to change SelectEven with SelectOdd (and vice versa) to switch left and right - cause i don't now for sure, if the even or odd field contains the left view .

Btw:
Most 3D software players can do such conversions in realtime, while playing the file. So if it's NOT strictly necessary to convert the 3D video, you can try such software players like the Stereoscopic Player, sView or Bino.