R-Type was on the Master System, not NES (though it was on Game Boy and Game Boy Color). The TG16, PSX, and X360/PS3 versions are better. Irem did release Image Fight on the NES, though, and it's good...
Anyway, NES shmups... there are a lot of them, though many are barely playable by modern standards. Who's up for a 25-level long game with only one powerup (that just doubles your rate of fire, nothing more), three lives, and no continues or saving? Anyone?
(That's Star Force, by the way. Not that there aren't far too many other games like that on the platform. And the game is fun... it's just insane to imagine actually beating it or something unless you're using savestates...)
Oh, Shmups.com has a complete list of shmups for the system, of course:
http://shmups.classicgaming.gamespy.com/xenocidefiles/nes.html . It only has review for a few of them, but they're very well worth checking out.
Anyway, my list.
Gradius - Has to be first on my list. Exceptional game, one of the best shmups ever... this game should be a must-own on the NES, even if there are 'better' versions out there. It's infamously difficult, with no continues, design that sends you back to the last checkpoint if you die, a brutal, nearly impossible slog to get your ship powered back up if you die, and a high difficulty level, but even so it truly is one of the best games ever in the genre. Graphics, music, design, gameplay... everything just works nearly perfectly. The Gradius power-up system is iconic and one of the genre's best, as well.
The Guardian Legend - Only half shmup, but all amazing. This is one of the best shooting games on the NES, and is another must-own. The whole game just works so well and is amazingly fun, and it's got (30-character password) saving, too, which is quite nice. Compile made great games, and this is one of their more unique titles... don't miss it!
Life Force - Salamander in Japan. Kind of like Gradius, but shorter, with at-point restarting when you die, continues, two-player simultaneous play, and vertical stages as well as horizontal. Awesome, as you would expect from classic Konami. The easier difficulty level and co-op mode are nice, particularly for people who aren't good at Gradius... note that the arcade and TG16 versions of Salamander, as well as Salamander 2 for arcade and PSX/Saturn (Japan only), have a much simpler powerup system where you just pick up powerups instead of using the Gradius style that NES Life Force/Salamander has. I much prefer the Gradius powerup system, so this is a big plus for this version... I'd rather have this for NES than TG16 for sure, because of that.
Gun Nac - Another great Compile shooter... this was their last NES game, and they clearly had learned with time. This one has their best presentation on the system, with better graphics and effects, some great weapons, and more. The US version had a few things cut (such as a couple scenes from the intro... when the background image freezes for an oddly long time, while the story continues below? Yeah, that's because they thought that the scenes there (one of a Shinto priestess casting some spell) were too Japanese to leave in... so they just left it on the previous one for a long time. Oh well. Not one of the easier ones to find, but well worth it...
Other games of note, US releases
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Xexyz (Another half-shmup like The Guardian Legend, except with shorter shmup segments, and side-scrolling action-RPG main game segments. From Hudson, and really good, if mostly for the whole game and not just the shmup parts. Has password save, and is definitely recommended!)
Air Fortress (HAL's half-shmup. This one is half shmup, half side-scrolling jetpack action game. Simple graphics and sound, but with good gameplay. I like this one a lot, but it does get pretty hard later on... fortunately it has passwords to save your progress.)
S.C.A.T. (reminds me a bit of Forgotten Worlds, probably because of the flying-guys characters... has 2-player simultaneous, too. A good game for sure.)
Stinger (Actually Twinbee. 3-player in Japan I believe, but just 2 here, likely because it came out before the multitaps. Still good stuff... this is Konami, after all.

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Image Fight (The Irem game that actually did come out on the NES. Quite good game, as I said. The NES version is of only moderate difficulty and is definitely slow paced, and has some very weird failed attempts at music playing in the background, but I liked it anyway... it may be slow at times, but overall it's fun and beatable, which is nice for a NES shmup. It has 2 player, but alternating only. This one's cheap, pick it up. (It's also on the TG16 in Japan, and in arcades, but this was the one US home release... worst version of the game for sure, but as I said, still good enough to be worth the low price.

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Recca (though if you want an actual copy, the price is unbelievably high... but it's a stunning demonstration of what the NES can do, for sure! This is on the NES? A manic-style shooter with floods of enemies? Amazing...)
Star Soldier (Hudson's first NES shmup. Simple, frustrating game, more popular in Japan than here. Not bad, but nowhere near the rest of the Star Soldier series...)
Starship Hector (Hudson's other NES shmup. This is a pretty good game, a nice improvement! Has Xevious-style separate ground and air attack buttons.)
Abadox (unique visual theme... insanely hard, though.)
Star Force (negatives listed above...)
Zanac (Great gameplay, but the difficulty level that gets higher as you shoot is just stupid. If you actually shoot a lot, it gets impossibly hard very fast... this makes the game kind of not fun. Many like it anyway, but I'd rather play Compile's later titles...)
1942 and 1943 (1943 is much better, but 1942 is a classic, even if it is far too long and boring...)
Dragon Spirit (better on TG16, but fun here too.)
Fantasy Zone (Tengen's US version is definitely downgraded in graphics and sound compared with the Japanese release, which looks worse than the SMS version, but still it's decent, if you don't have an SMS or way to play the import version, that is... did this use some chips Tengen didn't have access to, explaining the downgrades (like with Rolling Thunder)?)
Legendary Wings (2-player simultaneous. Reasonably fun game, I think. Not as good as the arcade version, though.)
Alpha Mission (okay game from SNK. Kind of fun, if quite hard... has some Xevious elements.)
Xevious (a popular classic, but I've never been interested enough to get very far... oh well.)
Galaga (fine port of the classic, but this is on about fifty platforms...)
Twin Cobra (Tiger-Heli 2, essentially. Better on Genesis and PC Engine, but the NES version's okay, and MUCH easier than the other US release, on Genesis...)
Oh, Tiger-Heli and Sky Shark are decent. Both have the same flaw, though -- no ending. When you beat the last level, it simply loops around to the beginning without saying a word... Tiger-Heli is slow-paced and hard, too. Some people love Toaplan's shmups, but if this is what most of their games are like, I don't know if I like it that much. On NES Toaplan only had this and Twin Cobra, but they did a bunch in the arcades and Genesis. As I said though, I find this very slow and not too much fun, and a bunch of other Toaplan shmups are a lot like this... but their Genesis games are popular, and they inspired a bunch of more recent shmup developers. I don't know how much Tiger-Heli is worth playing, though... maybe a bit, but there are far better shmups on the platform.
Super Spy Hunter is a pretty fun shooter too. It's technically not a shmup because you can control your speed and stop, but other than that, it qualifies for sure. Quite good game, too, if hard as you expect from SunSoft.
Gyruss - Another game worth mentioning here. Not a true shmup because of the 'tube' design, but a pretty fun game... this is one of the best home ports of the game, too. Try it and see if you like it... it's not as good as Konami's other shooters, but it is interesting for sure.
Imports
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Parodius (JP/EU) - Comic Gradius. Good stuff, if better on SNES, TG16, etc.
Crisis Force (JP) (2-player simultaneous. Konami. Some of the system's best graphics. Play this!)
Gradius 2 - Gofer no Yabou (JP) (impressive technical effort, and a fantastic port for the system... the game's better on TGCD of course, but great here too.)
Over Horizon (JP/EU) - This is a really good, relatively little-known game. Get this game, it's one of the system's best shmups for sure! It's really too bad it wasn't released in the US... at least there is that European release, though, so you don't need an adapter to play it on a NES 2 or modded NES. (I have one of those adapters for Japanese games, but still, having more options is always great.)
B-Wings (JP)
etc. There are more.