i just bought a 1989 suzuki 500 gs yesterday!    it is my first bike and i want to fix it up a little.  the exhaust headers are very rusted, and since the pipes are all one piece i was thinking of buying a new set of pipes.  i found a site that said the jardine system on pipecity.com fits all years of the 500gs bikes.  is this true?  oh, and if i can use those pipes, do i have to rejet the carbs?

yes! Jardine fits all models. Yes 2, you have to rejet the carbs - just keep in mind that you won't regret that mod 
3. congrats on your purchase - you will have a lot of fun with that bike.
4. you could use sand paper and clean the headers unless they have holes in them. After sanding them you can paint 'em with hi-tem grill paint - black, silver or whatever you like... RED? 
good luck and be safe!
KaMeL

i think i will try to sand them down and paint them.  the pipes are $350... i only paid $500 for the bike hahaha.  do i literally use regular sand paper?  what grade?

Last time I repainted my exhaust, I used a wire wheel in my drill to knock all the rust off; it worked pretty well

There are several threads and a mention in the GSWiki about repainting the exhaust.
http://cgi.stanford.edu/~sanjayd/gs500/Main/Restoration

The first one has broken picture links, but the text is fine.

I removed the rust with emory cloth and painted with bar-b-que black high temp.
Any high temp paint will do IF the surface is prepped properly.