The 1988 game of the year is Super Mario Bros 3.
The runner up is Mega Man 2.
The master thread for all of these contests can be found here.

What do you believe to be the "Game of the Year" for 1988 and why?  Also, vote on "Game of the Year" for 1988. 

Altered Beast  (Arcade)
This popular arcade game had a port that was bundled with the Genesis during its early years.  It also has some meme worth dialogue like “Power Up” and “Rise From Your Grave”.

Chase HQ (Arcade)
This vehicular combat game was popular in the arcade and as a port on home computers.

John Madden Football (Apple II)
First entry in the extremely popular and long running Madden series.  EA Sports titles were important during the 16-bit era as EA gave more support to the Genesis than the SNES.  The Madden series has sold over 130 million copies as of 2018.

Pool of Radiance (Home Computers)
Earlier RPGs were essentially trying to bring the D&D experience to computers and consoles.  Finally in 1988 Dungeons and Dragons gets an officially licensed product using D&D rules.  Pool of Radiance was the first of several “gold box” D&D games in the late 80s and early 90s.  The Pool of Radiance series went on to sell over 800,000 copies worldwide.

Robocop (Arcade/Home Computers)
Robocop exploded onto both arcades and home computers in 1988.  The home computer version went on to sell over 1 million copies.

Ninja Gaiden (NES/Arcade)
Ninja Gaiden got both an arcade game and a NES game the same year.  The two games are completely different.  The arcade game is a beat em up while the NES game is a platformer.  While the arcade game performed well, the NES game is the more memorable of the two with its storytelling through cinematic cutscenes.

Arcade version:  https://www.youtube.com/watch?v=eFwqTePDQXQ

Super Mario Bros 3 (NES)
In 1985, Nintendo released the first Super Mario Bros, a game which revived the home console market in the US.  In 1988, just 3 years later, Super Mario Bros 3 would completely put the first game to shame.  SMB3 would go on the sell over 18 million copies on the NES.  It was also featured in the movie The Wizard about 2 months before the game's North American release.

TV Show Intro:  https://www.youtube.com/watch?v=goHwtY2DHMw
Common Commercial:  https://www.youtube.com/watch?v=HU80R7jGanE
The Wizard:  https://www.youtube.com/watch?v=TscjsNMvnDg

Mega Man 2 (NES)
Mega Man 1 was a brilliant idea for a game, but end result was unpolished.  The game didn’t sell well for Capcom, but the developers wanted to try again, and so they developed Mega Man 2 in their free time around other games.  The end result was much more polished and ended up making Mega Man a household name.  Mega Man 2 became the most popular entry in the Mega Man series (until Mega Man 11) selling over 1.5 million copies on the NES.

Keith Courage in Alpha Zones (PC Engine/TG16)
In 1987, a huge electronics company, NEC, decided to enter the home console market with the PC Engine in Japan (or Turbografix-16 in North America).  Keith Courage was bundled with the North American version of the system.

Other (please specify)
If you think another games deserves to be "Game of the Year" other than one of the 9 I listed above, then please vote “Other” and say your game in the comments.  If the "Other" category takes at least 2nd place and no other game gets at least 50% of the vote, then I will do a runoff vote including the most mentioned game(s) from the comments.

The winner of this vote will be decided Friday, Sept 22 at 11:59 EST.

Here are a few other notable games from 1988:

Bad Dudes (Arcade)
Last Ninja 2 (Home Computers)
Ultima 5 (Home Computers)
The Guardian Legend (NES)
Dragon Quest 3 (NES)
Space Harrier II (Genesis/Mega Drive)
Thunder Force 2 (X68000)

Mega Man 2 for me. Probably my favorite game of all time. SMB3 is a masterpiece as well.

Mega Man 2 and Ninja Gaiden (NES) are both too sadistical for me and tbh I consider the latter among the worst games I've played. Basicly the equivelant of a troll Mario Maker level.

Super Mario Bros. 3 is an easy choice and probably the game of the decade.

SNATCHER!

Tho the SCD version came later it has my fave song in any video game. The game is an adventure game that is one of Kojima's best. It's his take on Blade Runner. Like Policenauts and Zone of the Enders. Same universe as Metal Gear.

Other notable games off the top of my head that deserve a mention are Ys 2, Final Fantasy 2 (largely disliked now but notable nevertheless), Snatcher, Gradius 2, Nemesis 3, Parodius, King's Valley 2, and Aleste.

My GOTY is King's Valley 2:

Easiest post.

Super Mario Bros 3.

My 2nd most favorite 2D Mario!

Well, this one is probably the most clear-cut choice so far. SMB3 is going to win, the only game close to it from this year in my opinion is Mega Man 2. They're also probably the only two from the list that are consistently fun to play to this day, as most games from this period still tend to age quite poorly.

Sorry Wasteland, as much as I love Fallout 1/2, and Wasteland being their direct ancestor, I voted Pools of Radiance - not only it was AD&D game, but was also precursor to later Black Isle/BioWare games that went on to define isometric CRPGs.

Other great games from that year I remember are Laser Squad, direct ancestor of X-COM (UFO Enemy Unknown), Hostages (which was later compared to Rainbow Six), quite a few adventure games and last, but not least (since it's the game I played a lot) Carrier Command (mix of real time strategy and sim)

In 1988 I was playing FS 3.0

A massive leap over the second one. I was still playing this with the keyboard, making landing very hard.
Thanks to my dad having the latest hardware it ran a lot better than in this video.
I downloaded the manual from a BBS (the game was pirated :/) and printed the whole thing out in the smallest font on a matrix printer. It was a big stack of paper, the longest manual I had seen so far. A popular topic at school as well since a friend of mine was studying to get his small plane license for gliders. There was a recreational airport next to the town we grew up in.

But this year goes to SMB3. I didn't play that until much later since my first Ninendo hardware was a game boy before N64.