Well, let's count them up. Note that some glitches may be shared between two or more games in a generation.
Generation 1: 68 Total Known Glitches
Japanese Red/Blue: 64 Known Glitches
International Red/Blue: 58 Known Glitches
Yellow: 55 Known Glitches
Generation 2: 21 Total Known Glitches
Gold/Silver: 19 Known Glitches
Crystal: 18 Known Glitches
Generation 3: 22 Total Known Glitches
Ruby/Sapphire: 16 Known Glitches
Emerald: 8 Known Glitches
FR/LG: 6 Known Glitches
Generation 4: 68 Total Known Glitches
D/P: 30 Known Glitches
Platinum: 25 Known Glitches
HgSs: 26 Known Glitches
Generation 5: 59 Total Known Glitches
B/W: 41 Known Glitches
B2/W2: 34 Known Glitches
Generation 6: 10 Total Known Glitches
X/Y: 10 Known Glitches between all versions
Spin-Off Games: 13 Known Glitches
Pokemon Play It!: 2 Known Glitches
PMD Red/Blue Rescue Team: 2 Known Glitches
PMD EoT/EoD: 3 Known Glitches
PMD Gates To Infinity: 4 Known Glitches
Pokemon Ranger SoA: 1 Known Glitch
Pokemon Rumble Blast: 2 Known Glitches
For what game has the most, that goes to Red and Blue's Japanese Versions.
As for what system has the most, that goes to the GBC with 89 Total Glitches.
