Whats the best glue to use, to glue the rubber to the cone of the woofer, would silicon do the job??

Nope..Glue fumes can melt rubber...
You have to find a glue that is rubber safe...

If its on the outer edge anything will do, even masking tape and silastic, but expect the speaker to distort at higher volumes and if the damage is caused by age or sunlight/heat exposure, it will go in other places. How about a new one? Might be the best long term fix.

The stuff I use is Moyen RS-3087 Cement, comes in a JBL branded tube. You can pretty much use any sort of sealant though, shoe sole glue works well as its very pliable.

The speaker repairers glue of choice is Loctite Prism 480. Can be purchased in ~2ml tubes for $20, which is plenty to recone 2 12" subs.

Lift the flap that has come unglued, clean any crap off that might cause lumpiness, if it is a large unglued area that you can work in easily, it might be worth scraping back any crap from the metal basket and giving it a wipe over with metho (the metal, NOT the speaker rubber), and then apply the glue, place the loose rubber back in place, and use something to apply pressure like a small clamp.

Edit: looking at the Moyen stuff, it is pretty much same same as the Loctite product, so whichever is more easily accessible I guess! I buy my Loctite glue from Blackwood Atkins.

i ended up getting some of that loctite stuff for $18, it was hard to find, but seams to be working well