Regions, Versions and Platforms of MG MSX 1 & 2
In order of fastest to slowest
PAL Metal Gear Solid 3 Subsistence (Europe/Australia)
PAL plays at 50hz. This means that the game operates at a lower framerate than NTSC. However, to compensate for the lower framerate, Snake moves faster. He moves about 12% faster than NTSC 1). In addition, the PS2 version enables RNG manipulations for both Metal Gear 1 and 2. This is the fastest version to play. Due to this speed increase, PAL is separated on the leaderboards.
NTSC-U/J Metal Gear Solid 3 Subsistence (North America/Japan)
NTSC plays at 60hz. This means that the game operates at a higher framerate than PAL. Counter intuitively, NTSC is slower than PAL. You still have access to the RNG manipulations.
The Japanese language will lose around 7.1s vs the English language version. So NTSC EN is the recommended version to speedrun in the NTSC/HDC category.
HD Collection (All Regions)
Regardless of region, HD Collection operates at the speed of NTSC PS2. Again, PAL HD Collection does not have the speed of PAL MGS3! Additionally, the RNG manipulations are impossible on HD Collection on PS3, but not on Xbox. These two factors make the HD Collection the least favorable to play.
MSX Computer
The original versions of these games have different controls from the later ports. The framerate is rather poor, as the MSX struggles to run MG 2 particularly.
Conclusion
PAL PS2 offers the fastest version. PAL MG2 makes the runner's life a lot easier. PAL MG1 doesn't make as much of a difference in playability. If you must play NTSC, try to use Metal Gear Solid 3 Subsistence for the RNG Manipulations, or Xbox HD.