I've not really sold many of my "collection" games, mostly just games I fixed up to finance the collection. Those that I sort of regret selling, in order of "damn!", are:
1) Quicksilver. Just wasn't feeling the love on this one when I had it, especially with some of the shots, and though I loved the backglass, the green playfield didn't do it for me (yeah, I know -- lame excuse). But subsequently of course the game has become highly sought-after, and I now realize that it had the coolest Max Bonus reward sound-effects of any Stern: "wooop, wooop, wooop!" Would buy it back if that were possible
2) Flight 2000. Couldn't justify two wide-body Sterns (and I prefer my Cheetah, so shoot me), but it was a game that even pinball novices could get into. They are common though, so would be easy enough to replace.
3) Paragon. Wasn't really part of my collection, but I operated one I owned at my work. It used to pull in about $200/week at 25cents a play! Got really good at it, and loved the inlines. A friend wanted a game so I sold it to them. I still think it may be the best wide-body classic Bally (though my Embryon was prettier, it wasn't as much fun at all).
And I'm not even mentioning Star Gazer: Glad to see it go, and got top-dollar, so no complaints. Could sell it for kidneys now if I still had it, but still no regrets.