TOPS is a USAG program that identifies young girls that have the potential to become Elite. Some gyms go through the TOPS testing and implement the suggestions from the TOPS clinics just for those identified girls... Other gyms implement the suggestions for all gymnasts... and still others don't do the testing, but still implement the suggestions. The girls still compete JO, but they seem to be moved through compulsories as quickly as possible in order to get to Optionals sooner.
JO is a USAG Level program. There are 10 Levels and levels 1-5 are compulsory (all gymnasts in a level compete the same routines)... but USAG only requires a minimum score to move up starting with Level 4. Level 6 is a new Optional Level this year and it is not required... if the gymnast has the skills to go to Level 7, then they can skip level 6... it is a really watered down Optional level.
Xcel is a USAG program. It is less intense than JO and is an Optional Only program. From the lowest level, the girls are competing routines made up for them (some gyms choose to use the same basic routine for all their Bronze or a choice of 2-3 for them. At Silver, some gyms do a few options of music and others do all individual music and routines... for Gold, Platinum, and Diamond, they definitely get their own music and routines). Gold is the first division that has a required minimum score to move up.
USAIGC is not USAG affiliated. It is Optional routines only, but is designed for gymnasts to peak at the higher levels in High School (supposedly to prepare them to compete in college).
AAU is not USAG either, but they do use the USAG lower levels (compulsories) as the starting point. Districts can choose to use certain modifications if they want. I think AAU goes through Level 8 and then has an "Open Optionals" level... think- Level 9/10.
I know there are more, but these seem to be the most common mentioned on here.