A few more:

Obduction
"As you walk beside the lake on a cloudy night, a curious, organic artifact falls from the starry sky and inexplicably, without asking permission, transports you across the universe. You’ve been abducted from your cozy existence and added into an alien landscape with pieces of Earth from unexpected times and places."

X-COM: Terror from the Deep

Army Men: Toys in Space
back cover cover shows little grey men!

Tex Murphy: The Pandora Directive
"What is the truth behind the rumored UFO crash at Roswell? Why did the military suddenly shut down and seal off the Roswell complex? And why the frequent references to the lost Mayan civilization? "

Awesome finds! I went ahead and added all of three of the games that you suggested. Could you clarify which Space Quest game includes the UFO vehicle?

Thanks for all of the suggestions! I don't know how I missed adding X-Com Terror from the Deep to the GOGmix. It's been a while since I played that game, so I must have assumed it had more to do with Atlantis than aliens... anyways, correction made!

There are a couple parked out in Ulence Flats on Kerona in the first Space Quest game, both original and VGA remake. You can also see them in Space Quest IV when you time travel back to Space Quest I.

I suppose the original version of the Arcada and the Galaxy Galleria look a bit like flying saucers, but they are space stations rather than ships.

Space Quest - Outside Ulence Flats Bar
Space Quest - Tiny's Used Spacecraft
Space Quest VGA - Outside Rocket Bar (ship on the far left)
Space Quest IV - Outside Ulence Flats Bar

Thanks for pointing out the UFOs! I've added both games to the list!

I probably should have linked images of the holographic alien head too.

Space Quest I
Space Quest I VGA

I totally forgot to add the mention of the alien head. My bad! Everything is fixed now.

Carmageddon 1 has a UFO in one of the levels, Carmageddon 2 has a UFO and little green (or were they grey?) men exploring a pyramid in the "I Want to Bereave" level.

Thanks for the suggestion! I added both Carmageddon 1 & 2 to the list.

they do?
I've played those games a thousand times. I don't remember that.

I was certain for Carmageddon 2, though I was thinking it was a mission type and not a normal race. Checking to verify it I found that there is actually a UFO in one of the maps in the first game as well.

I try to verify how, when, and where aliens/UFOs/etc. appear in a GOG game before putting it on my GOGmix. If the reference appears as an Easter Egg (as many do) I try to provide information in my GOG list on how to access the secret.

Off topic, I've been pleasantly surprised by the number of fun Easter Eggs in older games. Apparently the first Carmageddon has a room dedicated to Twin Peaks, and Blood includes numerous references to the Shining, Duke Nukem, and other stuff.

It's been a while since I played through either of them, so they might be there and I just forgot.

Added Saints Row 2 to the mix since there is a UFO available in game.

*EDIT: Also added La-Mulana after much deliberation.

Updated to include Jazz Jackrabbit 2! There are some other minor tweaks since my last revision too.

A few minor edits in celebration of World UFO day. Keep watching the skies!