Since this thread has less G4 specific advice but was bumped recently, I'll give a simple rundown as many G4 are starting to appear at flea markets, thrifts, etc.
-A big killer for pony value is haircuts (sorry, show accuracy folks!). If you anticipate wanting to sell your collection in the far off future, it would be best to avoid cutting their hair. You can use various methods of twisting the hair and securing with elastics that will emulate the look of a forelock.
That said, a lot of the G4 ponies that are out right now don't have lots of collect-ability. Your run of the mill Twilight Sparkle isn't going to get you big bucks simply due to the sheer amount of them available. If you have a pony with a rooted forelock (two stripes of hair plugs running horizontally across the pony's forehead), do try to avoid cutting that hair (only Twilight Sparkle, Applejack, Rainbow Dash, and Cheerilee have this). These were early releases of the ponies and are more valuable than others. Certain variants of mane 6 ponies can also fetch some value in the future, such as the Cutie Mark Magic releases or the Rainbow Power, and you may want to avoid touching those. Any non-mane 6 ponies are up there in value as well.
-If you have brown coming out of the tail plug, that's tail rust! Ponies have metal in them to keep their tail in place, so this just means that some moisture got in and started to rust up the washer. You can remove the head and neck plug, and then remove the tail. Scrub with whitening toothpaste, or be careful with some rust remover. It may be a good idea to remove the metal washer entirely and replace with a ziptie to prevent tail rust in the future.
-The reboot/movie/G4.5 figures have VERY fragile necks. If you are removing the neck plug to customize or restore, do be very careful and patient when you are removing the plug or you will slice right through the plastic.
-You can rehair without using glue or a rehair tool! If you use a doll needle (a sewing needle would work as well) and some floss, you can thread a loop of floss into a hair plug, put some hair into the floss loop, and pull through. There are many tutorials on how to do this method.
-For some gunky hair, you can soften it up with fabric softener or conditioner. I've had more success with fabric softener on some of the newer hair, but a lot of it is dry as ever. If anyone can find a solution for this, please share...