One thing I'm picky about is having original circuit boards in the game. I'm not a stickler for matching serial numbers on the boards, though. If I get a game with an aftermarket board, I'll generally replace it and use the aftermarket board for diagnostics or just temporary replacements when I'm in the process of repairing a game.
I usually pick up project pins, so they will all need some degree of work. If I had the workshop space to be able to do a high-end restore on pins, I would--re-stenciling cabs and clear coating playfields.
But, I mainly settle for just cleaning, refurbishing, and making things look as nice as possible while also being as true to looking as close to original as possible. Though, granted, there are some good mods than can be done on the guts of the machine to make it more reliable, add certain capabilities (such as non-flickering LEDs) or to tastefully improve the look of the game in some way (uncle fester in the chair on TAF or the replacement palintir on LOTR). If I do add a mod, it has to be easily reversible.
So, I keep things mostly original (or looking faithful to the original), but color outside of the lines a little bit when it makes sense to me. Most of my games don't have a lot of serious hardcore collector value (like Krull, Kingpin, Loch Ness Monster, etc), so I'm not too worried.
In any case, there a lot of opinions on how far to go with a restore, or what things should/shouldn't be done on them. But, as long as you're not parting out when it can be repaired or making irreversible changes to a game (like re-theming it), most folks are ok with changes/additions that are reversible.