1. Rune Factory Frontier, this game was SO much fun, but didn't seem to really get much notice outside of a cult group of fans. It is, in my opinion, still the best game in the genre.
2. Disaster Day of Crisis.
3. Little King's Story
4. Fire Emblem: Radiant Dawk somehow doesn't get the praise of the Gamecube Fire Emblem, despite being much better.
5. Metroid: Other M. I liked this game better than the Primes, I am bewildered as to why there's so much negativity towards it.
6. ANNO: Dawn of Discovery, this game is easily the best introductory game to the Anno series, and while it won't satisfy everyone, I think most people would like this game better than the PC Anno games.
7. Fortune Street, a Mario meets Dragon Quest board game.
8. Wario Ware Smooth Moves
9. Sonic Colours
10. Muramasa: The Demon Blade
11. Scarface with Wiimote controls
12. Godfather with Wiimote controls
13. Endless Ocean/Forever Blue

There're a lot of hidden gems on the Wii. I know there were a bunch of survival and horror games that got largely ignored because they weren't Resident Evil.

Wii Music.

https://seanmalstrom.wordpress.com/2008/09/22/why-wii-music-is-genius/

https://www.theguardian.com/technology/gamesblog/2008/oct/28/nintendo-casualgaming

Forgot about these two. They got a bit of buzz back when they came out, but these days I suppose they qualify as overlooked. Both are well worth getting.

Yes! Zack & Wiki is criminally overlooked. One of the best adventure games of the last 15 years.

Let's see, what else?

Dead Space Extraction - an excellent and atmospheric light gun game.

No More Heroes - totally wacky but awesome combat and boss battles 

Wario Land: Shake It - lots of cool platforming mechanics and high replay value

Red Steel 2 - awesome motion controlled first person action

Muramasa - spectacular action RPG with two separate campaigns 

Honestly, there are so many overlooked Wii titles. Heck, I still have a pretty sizable Wii backlog to get through. Anyone who says the Wii library is small or insignificant isn't doing their homework.

At this point I'm not sure Wii really has any truly overlooked gems.  While I can still make lists for consoles like PS1 and PS2 that include games people don't remember, Wii lists seem to be full of the same stuff which is the same kinda games "should've sold better".

But anyway, my three suggestions are all here already:

Red Steel 2, Klonoa (it's just a remake, but still), Zack and Wiki to name a few.

The Last Story

I feel like Xenoblade stole all the attention to it.

I love both games (Xenoblade more, of course) but The Last Story has a better final boss (that plot twist tho)

Go Vacation

Let's TAP

Lost in Shadow

The Munchables

Pandora's Tower, Wario Land: Shake Dimension.

We're lucky that game came to the West AT ALL. Seriously, that had to be one of the biggest licensing nightmares in the history of video games. Tatsunoko doesn't have any branches outside of Japan, so all of its IPs are licensed out to other companies, with only a few of them going to the same ones. That's why we didn't get that fat genie in the West (I heard he sucked and was the worst character though) and why some of Tatsunoko's most marketable and well-known characters in the West like Speed Racer and the Samurai Pizza Cats were never in the game. Characters like Casshan and Yattaman had to have their name changed slightly, and because of property rights with theme music for some of the characters, generic background themes were used in Ultimate All Stars, the version that got an international release.

Don't get me wrong, I would love for it to come to the VC as well, because more people need to know what a more technical MvC game is like, or even have access to in the first place. I just would be very, very surprised if Capcom would want to go through that rigmarole again.