What is the recommended FPS for an NTSC Laserdisc? Does it matter? Set it 60fps, 30fps, 29.9fps, or another fps?

The "hardware" frame rate of USA NTSC video (from a USA laser disc player) is 59.94 fields or 29.97 frames per second. I do not know if Virtualdub does any of its own processing of captured video, though. If it does things such as deinterlacing, then the settings would be different for movies versus video-based TV shows, for example.

I capture LDs through VirtualDub all the time. VirtualDub 2 actually, use that if you're not. It's got a lot of improvements.

Capture at 720x480 29.97 FPS, then clip out all blue screen frames between disc sides.

If your LD is a film, use the inverse telecine (IVTC) filter on it after capture. Settings: Reduce frame rate, Top field first, Adaptive. This will restore the video to the film's original 23.976 FPS progressive picture the correct way.

If the original video source is actual NTSC like a TV show, use a normal deinterlace filter. I like yadif. Or if you use yadif 2x, it'll do a pretty nice job of giving you 60 FPS progressive output from the interlaced fields.

If my captured movie is widescreen, I also crop 60 lines off the top and 60 off the bottom. Then when I encode the final h264 mkv in ffmpeg, I pass the flag "-aspect 16:9". This makes the output much friendlier to modern widescreen displays.