When buying My Little Ponies, there are several things about the pony that will determine it's value. Hair, body condition, eyes, symbol, rattling are some of these. Remember, good quality photos of the pony on offer are a must.

Hair
Is very important. You want a pony whose hair is unfaded, silky, soft and unfrizzy. Some sellers may say soft but this does not necessarily mean unfrizzy.
Keep a look out for faded hair, the light pink on many of the G1 (first generation) ponies fades to white. Some sellers may try to pass it off as being a 'variant', but not many do.
Frizziness can often be tamed with a good quality hair moisturiser, providing it is not too severe.
Tail rust is a common problem and is due to the metal tail washer rusting and the rust staining the body and tail of a pony. An unfortunate problem that means the pony has maybe had a bit too much exposure to water.

Body
Obviously the ideal pony is a mark-free, unfaded pony. A lot of white ponies will turn off-white or gain a tan-coloured cast to them.
Some ponies may become victim to the 'smooze', the name of which is taken from the evil icky stuff in the original movie. What this means is that the pony will have tiny little black-brown dots all through her. Not very pretty.
Plastic 'cancer' is a result of degradation of the plastic I believe. It manifests as brown circles and marks at any place on the body of a pony. Unfortunately it is not removable.
Many marks may be removed with simple soap and water, so always try that first. Others may need something stronger like acetone/nail polish remover, but be warned, acetone will REMOVE SYMBOLS, PAINT AND EYES so make sure you are VERY careful when you use it, if you use it at all. Which I rarely do myself, and don't say I didn't warn you.
Other common faults include bite/chew marks (from little kids' teeth), pen/ink marks (often turn into ink smudges), highlighter (which fades in sunlight) and ingrained dirt (can often be removed).
A pony will fade if left in the sun/on a window sill for too long so make sure you display your ponies somewhere out of full sunlight.
Neon coloured ponies may have 'neon pony disease' which refers to discolouration of the plastic due to 'regrind'. There will be differently coloured spots throughout the body of the pony.

Eyes and Symbols
The best symbols are those that are unfaded, clear and unrubbed. They are often an important indicator of a pony's worth.
Eyes can often have rubs to them too so are important to know about. With the twinkle-eyed ponies, most seller's will say whether the iridescent coating that originally covered the eye is still intact, if it is then the pony will likely sell for more.
You may be able to retouch your pony's eyes/symbols if you have enough skill with a brush though I don't really recommend it, especially if you plan to sell the pony.

Restoration
Some ponies may be restored depending on their condition(hair replaced, eyes repainted etc.) although it is not that common. Sellers will usually say if this is the case, provided they were the ones who did the restoring that is. You can buy the same nylon hair that is used in My Little Ponies from several online stores if you need to replace the hair in your pony. There are several websites that detail how to reroot the hair of a pony, but I am also quite happy to explain how this is done.

Have fun collecting!