To clarify, stainless is much harder and stronger than most of the OEM fasteners, but it IS more brittle.
And unless you add some sort of anti-sieze to the threads, stainless will bond to the aluminum threads over time. After a few years, it will be impossible to remove without seriously damaging the aluminum part.
So you must use antisieze when using stainless, and you should not use stainless for critical, highly stressed applications like axles, brake caliper bolts, or connecting rod and transmission bolts.
An engineer with access to complete and accurate metallurgical data might make the decision that substituting stainless would be perfectly OK in many of these cases. However, the manufacturing data and specs for the original hardware are likely forever lost or unavailable, so you'd have to destroy a lot of bolts to become confident of their specs...
For 90% or more of the bolts and screws you encounter on a GS, stainless allen heads are the way to go, without question. I never remove or install anything without asking myself if I can find a stainless substitute with an allen head. Phillips head fasteners are never used in highly stressed applications, so you can pretty safely substitute all of these abominations.
The kits on eBay are a good start. Ace and Do It Best hardware stores usually have a decent selection at gawdawful prices, but they're OK if you just need a few bolts fast.
A couple of good online sources:
http://www.mcmaster.com
Great prices and fast shipping, but all the bolts come in bags of various quantities. I like having extras anyway.
http://www.mmsacc-stainless.com/
You can order what you need here via fax or phone, and they offer polishing for what seem to be reasonable fees. If you can't find what you need in the lists online, you can call and they'll probably be able to find or make it for you.
And if you want to spend some serious money, Google for metric titanium bolts... yikes!
Remember, you spec bolts by the diameter and pitch of the threads only, not the head of the bolt or the wrench size. Length does NOT include the head, unless it is intended to be countersunk so that it sits flush or below the surface.
Here are a couple of sample bolt diagrams from McMaster that may be helpful to ponder:
http://bwringer.com/gs/92095A248L.gif
http://bwringer.com/gs/91292A125L.gif