Oh SAI? Yes, my friend uses SAI too. And she's a very good artist too! She's a classmate of mine who excels in both digital and traditional art. I'm going to ask her for a copy of SAI again. I lost the copy because my lappy broke ;-; Also, I've had experience with using mouse in drawing and it's painful for my wrist.
I asked what app is best for iOS because I'm going to get one.
It kinda just .. depends on you I think, everyone has a preference to what program to use (I use photoshop because I've used it the longest and know it the most) a digital program is just a tool, like any tool you can get really good at it the more you use it.
BUT, here's some programs to try out:
Photoshop or Creative Cloud (they're pricey.. like .. hundreds and hundreds of dollars if you want to get it legally lol but it's my favourite?)
Paint Tool Sai currently only works for PC I believe ? but its $80
Medibang and I think GIMP are free!
Clip Studio Paint has a lot of things that manga needs (speedlines, speech bubbles, 3d tools, toning, etc) and if you get it on sale its only $20 they have the sale a lot .
Hope that helps! 
Medibang is good if you're gonna switch between iOS and computer since it lets you store your WIPs on a cloud. Not to mention it has features built for making comics. And, yes, to top all that off it's free.
idk how it compares to SAI and it doesn't have some editing features like Photoshop but w/e.
I love Clip Studio Paint so much so maybe you'll like it too? I actually have Sai but I never use it XO There's also Krita, which is a free program! It's a tad cumbersome, but I say it's worth trying out, and I know a few AMAZING artists who use it.
If you want an ios program, I would check out medibang paint, it's pretty cool! I also like ibis paint on ios, mainly just because it records your art process.
I mainly use Clip Studio Paint because its function as a painting tool is much better than other programs I used. But I also think Photoshop is good in terms of effects and stylizing artworks. In short:
Clip Studio Paint: Good if you know how to paint in real-life, and want to do a high quality artworks for comic. Other than that, it has a good manga-like features that you could use (speech bubble, creating frames, action/movement linework, etc)
Photoshop: Good if you know how to create your own brush (or download/use brushes). You could do so much with Photoshop if you know how to. So it's kinda like a wild card.
Sai Tool: I only used it couple times... It's function as a painting tool is somewhat between Clip Studio and Photoshop. But its kinda like.... there's limit to what you can do? It will create the same pixiv looking drawings... so I don't recommend it if you want to do drawings/paintings professionally.
I CAN NOT promo this program enough yet still I have never met anyone else who uses it. It's Mac exclusive, but it's the best program I have ever used and I have used everything. Clip studio, photoshop, Sai, and more.
The program is called Pixelmator and it has the cleanest, crispest quality lines of any program out there. It has everything you could ever need and is extremely user friendly. I love it so much, I wish people would start using it, it's an amazing program.
for a computer gimp is okay, I've used it, it's like photoshop's idiotic cousin. I've been using fire alpaca for line art because photoshop is garbage for line art and my version of illustrator is broken. Fire alpaca is a great free alternative to sai.
I don't know for ios which is good, every program I used wants cold hard cash to make it work.
So I'm not sure if you're talking about computer or iPad/iPhone applications - most people on this thread have been talking about computer programs, but two iPad apps (not sure if they support iPhone's really tiny screen) that are pretty good (layers, brushes, etc.) are:
Procreate: since today, about 6$. Pretty good, has a lot of functionalities for an iPad app. I think now you can save to iCloud if you want to carry your drawings around on multiple devices (not sure if it saves layers and the like, though). One of my friend uses it a lot, her art turns out pretty good and clean.
Medibang has an app, (free!) and if you create an account, you can sync up your works on a cloud server (zetina already talked about this: yeah, you can switch between the iPad app and the computer app, pretty cool, I think). I just got the app, but I've been drawing with the computer version for a while now, and I highly recommend the program. And I personally like the brushes, they're suited for my drawing style.
I hope this helps, if you're talking about apps for your mobile devices...
for Motsuro project1 I use a mixture of Mypaint, paint.net, and gimp, and ms paint. Mypaint for actually painting, paint.net for clean frames and screentones, gimp for more screentones, and ms paint fo rtext!!! all of which are free. haha.
I just use Photoshop because it's the program I've used the longest and I'm just so used to it, though I know it can be daunting for beginners. But its complexity is what gives it the most flexibility IMO.
I tried to use Manga Studio and used the EX4 version. I really couldn't get into it despite several repeated attempts. The learning curve is quite steep, but it's definitely cheaper than Photoshop and is a decent program. I heard that the newest version is a vast improvement, so if you haven't already I'd recommend you give it a try.
Sai Paint Tool isn't bad either and is great for crisp line art. It's also a lightweight program which IMO is both a plus and a minus. The disadvantage is that it doesn't allow you to manipulate your images as well as photoshop. It's meant to be just a drawing and painting program.
Usually people make comics using Photoshop, but I don't like it so much, I prefer Krita, it's a free program and easy to use, but it has its pros and cons because it's perfect for making manga comics but I need to use photoshop to put it on a jpeg format (but maybe it's just me that don't understand how to do it)
when I drew on my iPad, I used an app called Procreate a lot. If I ever want to draw on my iPad, I always reach for that app =)
As some people have suggested, Sketchbook is pretty nice too!
Photoshop is absolutely lovely, but if you can't afford the 10$ a month or so, Paint.Net is a very worthy substitute. And it's free.
Clip Studio Paint is the best for comic creation in my opinion. It creates word bubbles and comic panels so easily. I love it and use it for my comics every day!
I use my ipad to make art since I cant afford a tablet + a good pc art program ^^" When I make more painted looking type of art (like realistic portraits) I use procreate, and for my webcomic I use ibispaint x! Procreate, as ive seen its been said here, is about 6 dollars now. Ibispaint x is free, although to keep all the brushes you gotta pay, but you can get around this by watching a quick ad and it unlocks all the brushes for 18 hours, so I find this app very useful ^^
