Lessee, there are a few things I do to all Estes kits, most have been mentioned already:
Replace the tri-fold with Kevlar thread anchored to the motor mount tube.
Sometimes I just use a long Kevlar shock cord, on others I'll use elastic on the nose cone end.
I prefer to friction mount the motors on my LPR stuff, so I almost never use the motor hooks.
If I do use the motor hook I cut off the big tab thingy so that it is like the old style hooks.
I use nylon chutes, usually a Top Flight thin-mil X-form in an appropriate size for conditions.
Often I will do one or more of the following:
Upgrade the kit motor mount to a larger size.
Convert to through the wall fins.
Built up fins for a more accurate airfoil on scale models.
Add scale details not included with the kit like wraps, rivet and bolt heads, weld seams, etc.
Use rail guides on anything with a 29mm mount (stock or modded).
Convert appropriate kits, like a Nike X or Red Nova to multi-stage.
On the newer kits that have a short tube for the fin can coupled to a long body tube, I glue the fins and motor mount to the long tube and use the shorter tube as a payload bay.
Other times I just use the tubes and the nose cone to scratch build something completely and utterly unrelated to anything even resembling the picture on the bag...