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SolveIt comments on Open thread Jan. 5-11, 2015 - Less Wrong Discussion
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I can code, as in I can do pretty much any calculation I want and have little problem on school assignments. However, I don't know how to get from here to making applications that don't look like they've been drawn in MS Paint. Does anyone know a good resource on getting from "I can write code that'll run on command line" to "I can make nice-looking stuff my grandmother could use"?
Buy a good textbook on visual design principles. I don't have a recommendation in this area, so you'll have to do some homework to find the right one. Start looking at the work of professional designers in the area you're interested in. I use a blogroll for this, but you can pick your own path. The design section of my RSS currently consists of abduzeedo, design milk, and grain edit. For mock-up tools, I like Inkscape a lot. It's free and mock-ups are mostly about the text, shape, and pen tools anyways. In the area of raster graphics, I haven't seen any good alternatives to Photoshop; not that I've been looking. You can also look into some user experience stuff too, but that strikes me as overrated. After that, which programming tools you pick up will depend on your needs.
I've used The bootstrap framework to make web apps that don't look horribly ugly. Learning all the things you'd need to make apps that use that (so a bit of JS, CSS, HTML, etc. as sixesandseven says) would probably be a good start. (It would be probably easier than trying to make good-looking CSS from scratch, which is more of a pain).
Bootstrap is particularly good if you're a design doofus and have minimal knowledge of web standards, accessibility, fluid layouts, etc.
I'm sure ancestor commenters know this, but it's worth mentioning that design is a distinct discipline which doesn't come for free when you learn to code.
This might be a disappointing answer, but HTML, CSS and JavaScript are extremely valuable skills if you want to throw together accessible GUI applications.
You can try learning how to create mobile apps, seems like a very useful skill. For example, Android programming: https://developer.android.com/training/index.html
Depending on how much you want to invest in aesthetics vs. simply producing a user-friendly GUI, Visual Studio takes almost all of the tricky work out of producing basic GUIs (whether you're working in Visual Basic or C++) and is an easy go-to solution especially since it's now free for individuals, even for commercial use (still requires Windows though; I don't have a lot of experience writing GUI apps for other desktop OSes). The results will likely look somewhere between utilitarian and just ugly until/unless you learn some UI design aesthetics and expend the effort to apply them, but even there tools such as Blend exist to help out (especially on mobile, but some of that stuff can be applied to PC software too).