I currently have a 100amp main service box but it is all full and some are even doubled up.I'm wondering if i can hook up a 100amp subpanel off of it?
Certainly, that is what sub-panels are for.
If so what size wire to go with?
The wire should be #3 copper for 100 amps and a 100 amp two pole breaker to feed it.
Do I have to use conduit between the two, or does it have to exit the bottom of main to top if subpanel?
No, and no. You choose where to install it and what wiring method to employ. It just cannot be higher than 6 1/2' to the top of the highest breaker.
Also all I'm seeing at local store is 100 amp main boxes. Is that allowable by code to use as a sub?
Yes, just don't use the bonding screw or strap.