I think all of these have been mentioned, but I will second the following (in no particular order)
1. Gilmour Live at Pompeii - The Black Strat (still more or less stock) > Si Fuzz Face > Colorsound Overdriver > Hiwatts through his WEM cabs and WEM spinning speakers, Binson Echorec. Gorgeous, gorgeous use of that technology and still very clearly a Strat. Made me want to buy one after being a Tune-O-Matic and Tele guy for a very long time.
2. Jimi Hendrix throughout Electric Ladyland and the final days of the Experience on through to the Woodstock-era band. I won't rehash the rig(s), but c'mon!!
3. Eric Clapton using 'blackie' on the Layla album - to think it was recorded through a bunch of Fender Champs and similar small amps but still sounds this huge is very inspirational for me.
4. Jeff Beck ever since he moved to strats for good back in, what - the BBB era? His rig is (and has typically been) deceptively simple, but he wrings every possible thing he can out of a strat, and again, what he does you can really only achieve on a traditional strat setup.
5. Rory Gallagher - yup.
6. Ritchie Blackmore - I would say his was a very specific and groundbreaking tone for the time, and you simply couldn't do what he did or sound how he did without using a Strat. Classic strat tone.
7. Buddy Holly - Hello. He's one of the main reasons why people fell in love with Strat tone to begin with.
8. Robbie Robertson - Not my favorite player by any means, but he made a strat do some very unique things within his style and deserves mention here.
9. Big Star and the Impressions are also very, very good choices. I will also mention Ernie Isley's and (some) of Eddie Hazel's tones in the early 70's as being especially great.
10. I'm honestly really bored by SRV, but he did take many cues from Hendrix yet map out his own tonal landscapes, which is admirable.
And despite how BRILLIANT the rest of the show is, Jimmy Page's work on the strat on the Knebworth show is kinda groady, imho.