if you want to go the upgrade route:
tuners (they often use very cheap ones that cause tuning problems)
nut (the plastic ones suck tonally)
saddles (standard ones are poorly machined and contribute to tuning problems)
trem block (the squier's standard blocks are generally weight reduced and made out of substandard materials, you want to go for the solid steel or brass ones)
electronics (tone caps, pots, jacks, switches)
pickups (duh, toneriders are well priced and recommended)
you can get these things from:
http://www.guitarfetish.com/ (cheap wholesale stuff, probably not a whole lot better than whats on your guitar)
http://www.stewmac.com/ (diverse range, a little more expensive)
http://www.acmeguitarworks.com/ (good quality stuff, pretty expensive)
http://www.lmii.com/Default.asp (varies, the shipping is quite expensive)
http://www.tonerider.co.za/