has anyone discovered a way to combat the intonation problem a strat has with the low e string? in almost any case, no matter how far back you set the saddle, a fretted note on the e will almost always sound sharp. i've gone so far as to remove the spring entirely and it's still a hair out. to compensate, i always tune my low e a little flat and strike it a little harder than the rest of the strings to increase the string pressure. (that sharpens the pitch of the open e)
thanx, jk.

Intonation problems on the low E on a strat with the stock trem are usually caused by the nut not being cut properly for the size of your E string. If you look closely at the string and how it sits on the nut, I'll bet you notice it is actually not sitting IN the slot but more on top of it. If you're using the standard .42 E string, this should not be the case but if you're using heavier strings it's pretty much guaranteed to be a problem. If you have the skill, get yourself a set of Nut files and file the nut so the string fits in the slot properly but ONLY do this if #1, you know what you're doing #2, you don't plan to switch to a lighter gauge strings and #3, the string is actually sitting on instead of in the slot.

Intonation on a Strat is a pain in the azz anyway but, if the strings fit the nut properly and everything else is setup correctly, if one string can be intonated they all should be able to.

One other thing, a bad string can cause intonation issues. I've had more than one instance where 1 string out of a set just would not intonate. Replacing that one string fixed it 99% of the time.

i've had the same problem... I had to not only remove the spring on the low E to move it back, but also the G string!
I'm currently using 11's for the extra sustain, but i'm seriously thinking of switching to 10's even though I dread the thought of having to reset the tremlo tension, truss-rod, etc... *sigh*

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UPDATE - I did switch back to 10s last night - resetting the tremlo tension (and especially the tremsetter) was a pain in the ass and I still need to readjust the action (which I'll be able to lower w/ out buzz! but i'm intonation was noticably better right away! guess I'll be playing 10s from now on...

You can also try to put some graphite into nut. You can use pencil .

Graphite is good, and easily gotten. I use a teflon gel made for trombone slides called slide-glide. It's the same as the teflon gel stuff you can get in gun shops.
Intonation on Strats is often due to the strings wearing away from the fretboard side of the nut and "taking off" from inside the nut. If your saddle is all the way back and the string is still sharp, look to the nut. It's also a good idea to check the distance of the pickups, especially the neck pickup. Too close and the magnetic field will actually create a false harmonic that makes the string sharp out.