Link - Lots of counter play is needed. He has some very safe aerials on block when spaced well with fair, nair, bair and zair. Zair is really serious in terms of space control. Focus Attack is good for dealing with Zair and his grounded buttons of ftilt and dtilt. FA is also good for dealing with boomerangs and arrows. Generally aerial FADC is good because you can tank a hit then dash in and once you land you can still keep closing space. Also using FA on the ground opens you up for that tether grab into d-throw set-ups, even at mid range due to his grabs length. Generally you want to play your spacing a bit closer since his close range options are slower then yous while his mid range options are better. His ftilt hits on frame 15. Dtilt his on frame 11. Both are pretty safe at -6 and -2 on shield drop respectively. His jab is frame 7 and if he ends with the second hit he is only -4 on shield drop. Though at that spacing a JC aerial from shield might catch him or at least allow some pressure. I need to test that further. Don't just come at him from high in the air btw. His usmash and utilt are good anti airs. To close in you will want really solid defense and evasion. Be able to perfect shield projectiles then shield drop and continue walking forward. If he suddenly advances on you to disrupt your careful approach just be prepared to roll or spot dodge. More then likely he wants a grab. Bombs can be used against him. They do not blow up on block so you can block then snatch them and use them for your own offense/approach/mid range game. You could also just aim to catch them in mid air. Hadoukens aren't that good since all his projectiles beat them as well as zair destroying them easily. Just focus on closing space and staying vigilant for his zoning. No wall is impenetrable. Every zoner has holes you can exploit.
Samus - Similar rules of engagement to Link. Be on the look out for Zair. Missiles are a bit easier to deal with then Links zoning. She can penetrate your spacing not only with dash grab, but a nice dash attack as well. Her ftilt and dtilt have good start up at 8 and 6 frames, but are very unsafe on shield drop at -11 and -18. She does have a 3 frame jab however which is -4 on shield drop. Her dash attack is also pretty dang fast, hitting on frame 8. Charge shot also makes mid range dangerous when she has it and demands high level reactions so you can dodge or move out of the way if need be. Ideal range is inside her tilt range but far enough that an up b wont catch you, at least not consistently. Her up b is a solid defensive option that can shut down overzealous aerial approaches. At this range she can still jab, but her jab is not really scary and really only leads to mix-ups. However, here you can pressure with d-smash which she can't punish well even with a tether grab as long as you are spaced well. At this range she also has to be smart with defensive options. Expect jump back zair to reset her spacing and spot dodges as defensive maneuvers. If she rolls thats a free grab or dash shoryu.
Diddy - Tough stuff. The one match I think all Ryu mains agree that he loses even if its just slightly. Generally you want to be outside his dtilt range. His dtilt is frame 4 and very safe on shield drop at -2. It also confirms into grabs, another dtilt or smash attacks. It's one of the best footsie tools in the game. He has a great fair as well which comes out on frame 6 and has a huge hitbox. Though its not very safe. If you block it, you can to pressure him, even if it was an auto cancel. If he lands with it then hes boned. Make him feel pain. Monkey Flip gives him another strong mix-up tool. Since he can command grab from it or side kick, its easy to keep opponents guessing. Mix in his dominant grab game and you have a neutral monster. There is no easy way to deal with Diddy at mid/footsie distance. Shield is strong vs fair and will protect you vs dtilt, but will lose to his command grab and dash grab. Trying to stay loose is good sometimes with mixing in empty hops, but can outright lose to his huge fair. We havent even gotten into the standard gameplan of hold onto a banana and wait in shield, allowing Diddy to stay in control even when on defense. You need to know your best options. Generally, Ryus light ftilt will do work in this match. It can beat alot of Diddy's stuff head on since Ryus foot is intangible. It will beat dtilt, fair, monkey flip options and reckless dash grabs. Its active on frame 8 till frame 11. 4 frames. Really good stuff. You can also get follow ups at low percents. Beyond footsie range you can re-actively shoryu monkey flip options. So if you are fighting a diddy that gets flip happy at mid range, keep that option in your back pocket.
If you decide to mix in empty hops to keep him guessing then remember your fair will trade with his usually and so does bair. You win those trades in terms of damage. So dont be afraid to throw those out occasionally to keep him honest if you notice the diddy wants to fair in footsies. Focus Attack also craps all over his fair. Tank the hit then pop him in the jaw and get your combo/follow-up.
Shakunetsu hadouken is solid. His fair can beat it, but generally that only works if he already committed to it. Shaku can keep him suppressed and put fairly safe pressure on his shield. Shaku will lose to banana toss however so you may wish to stick to normal hadoukens when he is holding onto a banana. Speaking of which, banana holding diddy is tough to deal with. Just remember if he is holding onto that, then he can't play footsies with his dominant normals vs you. You can now dictate that aspect of the match. Just be mindful of nana toss out of shield. If you are close and Diddy is sitting in shield, then a quick dash grab can catch him off guard and give you advantage. Another trick is dash in then turn around but still SH towards Diddy so your back is facing him. Then come down with a fair. The sour spot fair or cross up fair for my SF vets is very safe on block. It will push the defender towards the direction Ryu is facing, and past him completely. This looks very awkward. An opponent may reflexively attempt to punish. In this case Diddy would toss the banana. Then you get a free d-smash very easily or dash grab for some stage control. Generally just remember Diddy with a banana usually is looking to punish something for free damage. If he simply throws the nana at your shield, most of the time you can just roll and reset to neutral and you block the banana.
Really have to know all your options in this match. I have beaten strong Diddy's and lost to strong Diddy's. Its a tough one, so never get down on yourself.
My apologies for the late response.