This script works if your emulator is setup to output all of the lines it should. Videos should either be output at the full 240 line height or padded to 240 for an even resize to 480 less the aspect ratio get all out of whack.
Also, imo, point resize looks better if you only resize to an even multiple of the original height and then use a bilinear resize down to the resolution you're going after.
NES/SNES 240 to 720? PointResize to height of 960 and a BilinearResize to 720.
NES/SNES 240 to 1080? PointResize to height of 1440 and a BilinearResize to 1080.
The other thing that irks me, and this is on just about every single NES/SNES encode (not just Flygon's), is that the aspect ratio is off. NES/SNES video should be padded with 16 pixels on the left of the video and 11 pixels on the right of the video and then resized to whatever width you're shooting for. Again, preferably using point in an even way and then using a bilinear to get your final width.
For reference I'm pulling pixel numbers for the nes/snes width from here
http://wiki.nesdev.com/w/index.php/NTSC_video
If you've ever captured video straight from an NES you'll see that the pulse pixel and bgcolor pixels are totally visible as seen here
http://www.youtube.com/watch?v=UCkTZoDbnTw
Different systems have different scanline breakdowns. NES/SNES is what I am most familiar with and if it helps us get more correct looking encodes I'm all for it. Take this all with a grain of salt if you're not all that concerned with the accuracy of the aspect ratio.
Hope some of this information helps you guys out.
PS @ Flygon: I appreciate the HD encodes you've been doing. You may want to start stowing away 60fps progressive encodes. 60fps at resolutions up to 720x480 are allowed in the standard Blu-Ray spec and 60fps encodes up to the full 1920x1080 are allowed in the Blu-Ray 3D spec. It doesn't necessarily have to be 3D content to take advantage of the frame rate improvements. Something tells me that YouTube and other sites won't be too far behind in supporting 60fps.