Within a Deep Forest (PC, Free)
Within a Deep Forest is a bit different from your typical Metroidvania game, since you play as a ball and must simply use your skill and reflexes to navigate difficult areas without dying. As you progress, you'll find new materials to transform into which will allow you to go to new places. The exploration is a bit lighter in this game than some, as there aren't any optional pickups to find and the different areas are all accessible from the same main hub area. Still, finding each area in the main hub can be challenging (in a good way).
Knytt Stories (PC, Free)
& Knytt Underground (PC, Wii U, PS3, Vita) (Full review)
Knytt Stories is mellow and pretty and has no focus on combat at all. It is purely exploration and platforming (which is often quite difficult). Each new ability will let you explore the vast worlds further. There are no bottomless pits and few endless skies in Knytt Stories; if you don't see a lava pit, it means you can go there and explore further. What really makes Knytt Stories shine is that anyone can create new "levels" for it, so there are tons of free games to play within the same engine. Knytt Underground is similar (though I haven't played it yet), and seems to combine some aspects of Within a Deep Forest as well.
An Untitled Story (PC, Free)
An Untitled Story was made by Matt Thorson, the same guy who made Give Up Robot, MoneySeize, RunMan, and other great free games. The graphics appear to be drawn in paint, which might turn you off to it, but it has a large world to explore, bosses to fight, and secrets to find. It holds its own just fine among other Metroidvania games.
You Have to Win the Game (PC, Free)
It's got really retro graphics and audio, but it plays like a dream. There are lots of hidden trinkets to find if you're going for 100% and lots of challenging platforming similar to that in Knytt Stories. Progression is usually fueled by activating different colored blocks, like you did with the switches in Super Mario World, and also by upgrading your own abilities, as usual. Check it out!
Shadow Complex (XBLA)
Disclaimer: I've only played the demo of Shadow Complex, but this game looks awesome and is one of the three or so games I'd want if I had a 360. Once again, it's like Metroid, but in a modern or futuristic - but not as futuristic as Metroid - setting. It also is more of a 2.5D game, since you can shoot enemies all around you, even though your own movement is limited to a 2D plane. So, like, buy it or something, 'cause I can't.
Guacamelee! (360, XB1, Wii U, PS3, PS4, Vita, PC) (Full Review)
|The Steam version has custom costumes. Batman makes this scene even more amusing.|
La-Mulana (PC, Wii Ware)
If you took the unforgiving nature of the original Castlevania games, combined it with the exploration of Symphony of the Night, the utter lack of hand-holding of the original Metroid, and threw in some puzzles like Myst's, only more enigmatic, you'd end up with La-Mulana. It's brutal, and unless you have loads of time on your hands, you're probably going to need a guide to figure out some of the puzzles, but even taking that into consideration, La-Mulana is a great game and worth playing.
Outland (PS3, XBLA)
I've just started playing this one and so far it's pretty awesome. It's similar to Guacamelee in a lot of ways, including the gimmick of swapping between light and dark in order to avoid damage, use certain platforms, and attack enemies. The art style is quite beautiful (although the music seems to be more atmospheric ambient sounds than melodic so far). It's also interesting in that many obstacles and enemy attacks shoot out unique patterns of many small bullets, very similar to what you'd see in a bullet hell shooter. So far, there seems to be less focus on exploration than other Metroidvania games have (the area maps are filled in from the start with a clear destination and optional areas rarely have more than a few extra coins), but it's still very fun and worth playing.
K.O.L.M. (Web, Free)
Onto the Flash games! K.O.L.M. stands for Kind Of Like Metroid, so... yeah, that's kind of what it's like. It's shorter than some games - it is a Flash game after all - but it has style. Rooms appear as if on a computer monitor and are often angled slightly with a cool 3D effect. It has a story too, and nice music, but basically it's about exploring and finding upgrades so you can explore more. What more could you want? There are also sequels, K.O.L.M.I.A.M. and KOLM 2.
Snailiad (Web, Free)
This game is better and longer than your typical Flash game. It is extremely reminiscent of Metroid, from its 8-bit graphics and music, to its Super Metroid-esque map and secrets. It can get pretty challenging as well. One thing that sets it apart is that, since you're a snail, you can climb up walls from the start. It's cool to see how the areas are designed so that there are still inaccessible areas, even with your apparently limitless mobility. I highly recommend this one.
Robot Wants... (series) (Web, Free: Kitty, Puppy, Fishy, Ice Cream)
Each "Robot Wants..." game is short, but oh, so sweet. It gets right to the core of the "run, jump, shoot, upgrade, and explore" formula, and it doesn't beat around the bush with unnecessary areas. If you only have a bit of time and need to get your Metroidvania fix, these games are the perfect place to start. They're just as fun as any other game, but won't take you as long to finish.
Ufouria: The Saga (NES, Wii VC)
may be an NES game, but it has more polish than most and stands the test of the time quite well; better than the original Metroid at any rate. If you haven't heard of it, it's probably because it was only released in Japan and Europe, which is a shame, since it's really good. The graphics are colorful and look to be inspired by Hello Kitty and the music is similarly upbeat, but make no mistake, Ufouria isn't a pushover. This game's abilities come not just as items, but as different characters with different abilities, who you can switch to from the pause menu. I'm willing to bet that a lot of you missed out on this one, so give it a try and miss out no longer!
ROM hacks (Free)
I hear ya, sometimes no substitute can fill the void of 2D Metroid in our lives. For those times, there are ROM hacks of existing Metroid games, and they're often just as good as the original. Sure, like, I guess the legality is a bit questionable, but really, just play some of these. If you're like me, you already own at least one copy of the originals anyway.
Reader suggested games:
Strider (PC, XBLA, XB1, PS3, PS4) - Suggested by /u/badgeometry via Reddit
It looks similar to Shadow Complex, but with a sword instead of guns. It's kind of like a modernized version of the NES Ninja Gaiden games turned into a Metroidvania game. It's actually a reboot of Strider for NES, which was basically just that. I hadn't heard of this until today, but after watching some gameplay, it's jumped to a high spot in my wishlist. Now I'm going to have to go play the original too.
Aquaria (PC, Mobile) - Suggested by /u/badgeometry via Reddit
How could I forget this one!? Aquaria is quite unique from other Metroidvania games because you play as a mermaid-like girl and swim through the primarily underwater world. The graphics and music are beautiful and just flying gracefully through the water is fun in itself. Underwater levels tend to get a bad rap among gamers, but Aquaria makes them a joy.
Insanely Twisted Shadow Planet (PC, XBLA) - Suggested by /u/rcubik via Reddit
Similar to Aquaria, you won't be exploring on foot in this game. Instead, you'll be flying through a totally sweet looking world, solving puzzles, and fighting things. It's hard to tell how Metroid-y it is from the Steam trailer, but rcubik says that it is, so I'll take his/her word for it. In any case, it still looks totally awesome.
Monster Tale (DS) - Suggested by /u/thaddius via Reddit
Monster Tale may look and sound kiddie, but it's got everything you love about the item collection and exploration of Metroid, some Pokemon-esque, SotN-esque familiars, and unexpected challenge (if IGN's review is to be believed). In spite of it's ho-hum title, Monster Tale looks to be quite an enjoyable gem of a game.
Aliens: Infestation (DS) - Suggested by Anonymous via the comments
It looks just like what you'd expect from a Metroid game, except set in the Aliens universe and more gruesome and filled with horror. Between this and Monster Tale, I'm starting to wonder how so many awesome looking DS games flew under my radar until now.
Valdis Story: Abyssal City (PC), A.R.E.S.: Extinction Agenda (PC), Bunny Must Die: Chelsea & The 7 Devils (PC), Dust: An Elysian Tail (PC), Rochard (PC)
- Suggested by /u/duswatts via Reddit
Additional games discovered after this post was originally written:
The Scheme (PC-88), Ori and the Blind Forest (PC, 360, XB1), Axiom Verge (PC, PS4)
Surely this can't be all of the Metroidvania games that are out there. If I missed one of your faves, suggest it in the comments and I just might add it to the list! And while we're at it with these game suggestions, you might want to check out these great N64 games you might've missed.