The final verdict...........

4th Virtua fighter
3rd Streets of rage
2nd Sonic
1st Shenmue

Reasons to follow.............

Sonic is their best seller but theres been too many dire games based around him for me to say its their best franchise.

The ones that come to mind for me are JSR, Space Channel 5, Panzer dragoon and so on, mainly becasue they havent reciently tried to revive them and made a complete cock up of it, somethin thats becoming incredibly frequent by Sega.

Out of all their franchises i think VF is the only one thats been running with regular 'updates' and stays consistant in quality.

I would love to see ShenMue continue on a HD console but theres always the worry that they will ruin it and spoil the series. I dont think Sega is in the position to put that much money into a project either.

The Sega that made the DC so fantastic seem to be dead in the water now, sadly.

 I agree that a lot of franchises have gone by the wayside, and yes , some are still incredible successes like Jet set radio and Virtua fighter....... but people like Yu suzuki, and Yuji naka should have been treated like royalty and kept at Sega at all costs.... they are still quite young and have soooooooo much to offer...... Sonic was an INCREDIBLE success for sega so why would you let the guy that made it a LEGENDARY franchise go so easily? and as for Yu suzuki... WOW  ,what a GENUIS.... outrun, Virtua fighter, SHENMUE.... and many many more...... losing those 2 alone was pure INSANITY on Segas part.... Yu suzuki wanted to make Shenmue online and he STATED that the story will come to a conclusion one way or another........ now picture this..... MR Naka and MR Suzuki still work at Sega....... who would not want to see Shenmue 3, Virtua fighter 6 with suzuki in charge and two incredible sequels like Sonic CD 2 and Sonic and  knuckles 2 with Naka in charge? these guys are PIONEERS..... the way i see it... pay them 7 figure salaries to keep them........... its lunacy.......