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To get the best results when converting footage from NTSC to PAL and PAL to NTSC, the Re:Vision Effects software solutions can't be beat. The Re:Vision Effects Effections Plus Bundle contains everything you'll need to do this, plus a lot more.

Tutorial Source: Re:Vision Effects

Converting NTSC to PAL using RE:Vision Effects products within After Effects

1. Import your NTSC interlaced material into After Effects.
2. Using AE's Interpret Footage command (in the File menu), make sure Separate Fields is OFF for the material (FieldsKit Deinterlacer will need this setting in order to do it's job).
3. Drop your NTSC footage into a 59.94 fps composition. Apply FieldsKit Deinterlacer, with its 'Timing Mode' set to > 2x FPS, 1 Frame per Field'. This will convert your interlaced into progressive material, 1 frame per original FIELD of input.
4. Drop the 59.94 fps composition into a 50fps NTSC resolution composition. Apply Twixtor. Set Twixtor's Input:Fields to None, Input:Frame Rate to 59.94. Twixtor will get the output frame rate (50 fps) from the composition's settings. (Note: If you're using Twixtor 3, drop the 59.94 fps composition into a 50fps NTSC resolution composition. Apply Twixtor. Set Twixtor's Input:Fields to None, Input: Frame Rate to 59.94, Output:Fields to None and and Output:Frame Rate to 50.)
5. Drop the 50fps NTSC resolution composition into a 50fps PAL sized composition. Apply any additional resizing/cropping as desired.
6. Drop the 50fps PAL-sized composition into a 25fps PAL-sized composition.
7. Render out using AE's field rendering set to upper or lower field first rendering, as is appropriate for your project.

Okay, you see that this works fine for a scene, but may look bad across scene cuts. Currently you'll need to cut your footage into individual scenes and perform the above process on each piece. We are working on providing solutions within Twixtor and FieldsKit to delineate scene cuts within the plug-ins themselves.

Converting PAL to NTSC

This is the same process, but reversing the frame-per-second and sizing operations.

1. Import your PAL interlaced material into After Effects.
2. Using AE's Interpret Footage command (in the File menu), make sure Separate Fields is OFF for the material (FieldsKit Deinterlacer will need this setting in order to do it's job).
3. Drop your PAL footage into a 50 fps composition. Apply FieldsKit Deinterlacer, with its 'Timing Mode' set to > 2x FPS, 1 Frame per Field'. This will convert your interlaced into progressive material, 1 frame per original FIELD of input.
4. Drop the 50 fps composition into a 59.94fps PAL resolution composition. Apply Twixtor. Set Twixtor's Input:Fields to None, Input: Frame Rate to 50, Output:Fields to None and and Output:Frame Rate to 59.94. (Note: If you're using Twixtor 3, drop the 50 fps composition into a 59.97 fps PAL resolution composition. Apply Twixtor. Set Twixtor's Input:Fields to None, Input:Frame Rate to 50, Output:Fields to None and and Output:Frame Rate to 59.94.)
5. Drop the 59.94fps PAL resolution composition into a 50fps NTSC sized composition. Apply any additional resizing/cropping as desired.
6. Drop the 59.94 fps NTSC-sized composition into a 29.97 fps NTSC-sized composition.
7. Render out using AE's field rendering set to upper or lower field first rendering, as is appropriate for your project.

Okay, you see that this works fine for a scene, but may look bad across scene cuts. Currently you'll need to cut your footage into individual scenes and perform the above process on each piece. We are working on providing solutions within Twixtor and FieldsKit to delineate scene cuts within the plug-ins themselves.