In your House matches?
A whole bunch of Shawn Michaels, I'm sure. Depending on what you count as In Your House, clearly Shawn v. UT would occupy a couple of the top spots. If not, I'd go:
1. Shawn v. Mankind
2. Shawn v. Jarrett
3. Shawn v. Diesel
4. Bret v. Bulldog bloodbath
5. Canadian Stampede Ten-Man
6. Taka v. Great Sasuke
7. Final Four
8. Undertaker v. Mankind (Buried Alive)
9. Undertaker v. Mankind (Revenge of the Taker)
10. Bret v. Hakushi
If you want to include the post-Ground Zero shows, insert Shawn v. Undertaker HITC at #1 and the GZ match at, say, #7.
Clash of the Champion matches?
1. Flair v. Steamboat
2. Flair v. Funk
3. Flair v. Sting
4. Midnights v. Fantastics
5. Enforcers v. Steamboat & Rhodes
6. Steamboat v. Austin (US title)
7. Blonds v. Steamboat & Douglas
8. Midnights v. Flair & Windham
9. Dustin & Windham v. Steamboat & Douglas
10. Thundercage six-man
Clearly I'm very biased towards the early Crockett version and tag matches in general, but DUH.