Best common table canon? Best rules to use, source guide, common tweaks/homebrew?

[Kurald Galain]

Which books hold the best versions of rules?

The PHB1 is the one with the best and most-playtested rules. You'll just have to import the expertise feats, and certain classes (e.g. Paladin) need their Foo Power book to have enough power choices. I would ignore the DMG1, which doesn't contain rules so much as it contains DM'ing advice which you can get from plenty of other places.
The best iteration of SC is to just run skill encounters exactly like you would in any other RPG, and then call them an "SC"; so that's another reason not to use DMG.
I'd add PHB2 for some additional classes, but almost none of the splatbooks contains any base rules worth mentioning, until the reboot in 4.5.

How many iterations of magic missile are there, and is there any benefit to including them as different choices?

I think three. There is some value in including the autohit version (from HOFK) for the sake of diversity, but frankly it's not very good.

What's the best monster stat construction

MM3.