Basically, it would depend on your preferences as well as type of play. You also have to take into account the hitbox size of the character and speed. For example, while MarisaC may be the strongest in MoF, her larger hitbox may put her below ReimuB in your preference.
As for me, this is my rating, I suppose... I will list them in "tiers", high-tier, mid-tier, and low-tier. EoSD is an exception however, as I feel all the shots are mostly balanced in that game.
I'll only rate them in a survival sense. Scoring play is completely different and changes many things. It would take too long to list both (and I'm not knowledgeable about every games' scoring systems, and lack experience to make those judgements)
EoSD: ReimuB > ReimuA > MarisaA > MarisaB
Now, you may be wondering. Why is MarisaA on the third spot? One word. Patchouli. Because her Patchouli fight is notably difficult compared to the other shots, I would place them above her. ReimuB is pretty great with her powerful focused shotgun, and ReimuA's homing helps with Remilia's fight (I'm looking at you, Scarlet Meister!)
PCB: High Tier: ReimuB, MarisaA, SakuyaA
ReimuB's unfocused shotgun and haxbox put her in a high spot. Her spread also helps against stages. MarisaA's raw power and ability to gain lots of Cherry+ for borders puts her high up. And SakuyaA's homing and ability to not even have to stay under bosses allows her to cheese many attacks by just going into the corner area and dodging. Oh, and she's Sakuya, and gets lots of bombs.
Mid Tier: SakuyaB
SakuyaB is only below SakuyaA just because she's a little quirky and harder to use. Although she is stronger, and gets the benefits of 4 bombs, I'd still put her as mid-tier. But this is subjective and I would totally understand if others placed her on the high-tier spot.
Low Tier: MarisaB, ReimuA
Now, just because they are Low-tier, does not necessarily mean they are bad. MarisaB struggles due to having less power than MarisaA and her terrible unfocused shot (It's hard to get any cherry+ from her). It's not enough to counter the 2-bomb limit. ReimuA is relatively weak. The only benefit is that she has a haxbox and does really well on stage 6's opener spam. She's not recommended to use for survival unless you're already comfortable with the games patterns, to the point where the only thing stopping you IS said spam. (ugh)
IN: (I really lack experience in this game to rate these shots, but I'll try anyway. I'll only rate teams though)
High Tier: Border Team, Scarlet Team, Ghost Team
Not only are they both strong, but they have nice versatility. Ran can lock onto enemies for great homing damage, and Remilia's familiars can be used to strategically cheese stages and she's still pretty powerful for bosses. Youmu is really awesome and Yuyuko trivializes stages. They also gain a bomb after each stage if you used a lot of bombs, so that's nice. And Youmu's slash bomb is pretty good at insta-killing the hard parts. I actually used these two on my first clear of this game on Lunatic due to how great they were.
Low Tier: Magic Team.
You already know why they are here. No explanation needed.
Mountain of Faith:
High Tier: ReimuB, MarisaC
Both are very strong shots! ReimuB has a haxbox, but MarisaC makes up for the bigger hitbox with her nice, strong, and versatile shot. Her options can be placed to make stages easier and her power can speed through bosses. ReimuB's needles practically destroy everything but as a lesser level than MarisaC.
Mid Tier: ReimuA, MarisaB (not bugged)
ReimuA lacks power, but her homing does help for stages. MarisaB's piercing is pretty nice and she's not too weak either.
Low Tier: ReimuC, MarisaA
ReimuC is only strong if you shotgun. And unless you're highly experienced at the game, it'll be hard to do so. Also, what's the point of that unfocused shot? :V
MarisaA is rather weak and her options are weird and don't really help her out much in stages. Her spread is low if you're maximizing her damage by having all options below Marisa, but you can at least spread the options apart for more spread, but you sacrifice power...
Subterranean Animism:
High Tier: ReimuA, MarisaA, MarisaB
These shots are great. ReimuA has that awesome power and haxbox and gapping. Her bomb is amazing and fun to graze with as well. MarisaA has strong unfocused power and her focused shot trivialize stages. Also, that point blank bomb... MarisaB is very versatile and can really help on stages, and her bomb isn't half bad either. All great choices.
Mid-Tier: ReimuC, ReimuB
ReimuC's bomb is strong, and her main shot isn't too bad either. It's too bad it's annoying to work with. (Although an experienced user of the shot won't have any problem with that). Also. Her Satori fight is rather difficult. ReimuB is pretty weak and her homing hardly homes at all. It's like a powered down forward focused shot and her slow shots make things like Parsee's second spell annoying.
Low-tier: MarisaC
Unfortunately, despite her awesome power. Her marisa haxbox and being bad at stages puts her low. Her bomb is nice though, though her Satori fight in my opinion is also the hardest, so that's annoying.
Undefined Fantastic Object:
High Tier:
ReimuA, ReimuB, SanaeB
ReimuA's power is awesome. Her bomb is strong, and she has the nice haxbox. ReimuB may not be the strongest, but she's still relatively powerful. Her haxbox is an added bonus. And she's also very good for stages. SanaeB has that awesome bomb, and is great for UFO collecting. Although, she lacks a bit of power for bosses, she does have a nice shotgun. And she's pretty good at Byakuren as well.
Mid tier:
SanaeA, MarisaA
MarisaA has piercing which is godlike in this game, as it can kill UFOs well. Her spread is nice too, as the lasers spread far apart when unfocused. Her focused shot is pretty powerful as well.
SanaeA is about the same power as SanaeB, but with weaker bomb. She does have the advantage of homing, so she can do good damage when not under the boss.
Low-tier:
MarisaB. Won't even bother saying why. You know why.
TD:
High Tier: Reimu, Youmu
Reimu has godly homing for stages, and great needles for bosses. Haxbox, trance autocollecting everything. What's not to love? Youmu basically trivializes all stages and Seiga with her slash. If you know how to use her well she's pretty great. Although she struggles with Miko a bit due to being pushed so far down the screen on most attacks.
Mid-Tier: Marisa
Marisa has nice power, but doesn't beat Youmu or Reimu in that department. Her master spark is nice. And her trance is ultra crazy powerful, but in reality you're better off with Reimu. Youmu at least has unique things to make her stand out from Reimu. MArisa is a dumbed down Reimu with no homing and a bigger hitbox.
Low-tier: Sanae
Oh, ZUN. Sanae was so great in UFO. Why did you depower her in this game? Her shot is very, very weak. And her trance is also pretty weak. I actually believe that it's almost impossible to capture Yoshika's final spell with Sanae on Lunatic mode becuase of how much HP Yoshika has and how little power Sanae has.
DDC:
High Tier:
ReimuA, MarisaB, SakuyaA
ReimuA is the best shot type in Touhou history. She's so versatile for stages. Her shift spamming gohei is so powerful, and she generally makes DDC a pleasant experience., She can get so many cool 2.0 bonuses as well. She controls the game. She OWNS the game. SakuyaA has that crazy ultra broken point blank knife gun. she also has a border like bomb, and she SLOWS DOWN ENEMIES AND MAKES THEM FIRE LESS BULLETS AT A SLOWER PACE. GAME BREAKING.
MarisaB is very strong in raw power, and her bomb is just ultra broken.
Mid Tier: ReimuB
ReimuB's bomb is great, and at least she has homing. But she's a disgrace to all needle shots. Her power is very disappointing.
Low Tier: SakuyaB
She's very weak and her bomb doesn't do much for survival. This is a shot specifically made for scoring, and she pretty much breaks the game in the scoring department due to how much PIV she gets...
