I've seen many a custom controller guides floating around and to be quite frank, I'm a little bit appalled by most of them. I made 30 or so custom controllers over the summer, so I've pretty much got the technique down pat and wanted to share my knowledge.

The Basics

1. Take apart your controller - video for gamecube controller https://www.youtube.com/watch?v=cr3ShQxxwvQ
2. Clean the shell (and buttons, if you're painting those)
3. Sand down using 600 grit sandpaper, then wash and dry with a wet paper towel
4. Use a white primer as a base coat. If you've never spray painted before, here's a video on proper technique (https://www.youtube.com/watch?v=qB_MtpaMYaY). Doing a couple of very light coats is very important (don't worry if the first coat doesn't cover up all the paint) and remember to shake for a minute or two before spraying! I use rustoleum's white paint and primer in one and have very good results with it. Also keep in mind that if you're spraying buttons, DO IT VERY LIGHTLY AND FROM A DISTANCE. If you do it too close, you risk knocking buttons over and smudging the paint.
5. Wait 10-20 minutes for the primer to dry then do a few very light coats of your main color.
6. Seal the paint with a clear coat. I would argue that this is the most important step of spray painting. Hands down, the best clear coat you can use is an automotive spray paint clear coat. USC spray max high gloss clear coat works brilliantly and will not only ensure that your paint never chips, but makes your controller look super shiny and much more professional. It's essentially the difference between https://imgur.com/a/pDE3r and https://imgur.com/a/dhs8h. Sure, you can buy some krylon clear coat for $10 less, but don't think I won't know about it. I would do 2 coats and make sure you really get the side of the handles (where you're holding the controller). I would also use a respirator (that's respirator, not just a face mask) if you have one when using this clear coat, as the fumes are toxic. If you're making more than a few controllers, I would say it is without a doubt required, but if you're just making one and haven't got a respirator on hand, hold your breath and just go for it.
7. Do not let your clear coat dry outside unless it's protected from the wind somehow. If you have a garage, supply closet, or cellar no one is using, let it dry there. Drying it outside guarantees that little bits of dirt, pollen, ect will cling to it. Just trust me on this, this is the place where things go wrong the fastest. If you do happen to get little particles stuck on your controller, wait for it dry and then sand them out and respray.

Levelling Up - designs/decals

If you want a picture/letter design on your controller the two best options are vinyl decals and waterslide decals. Don't think you can put a sticker on the controller and paint over. If it's your first time painting, you'll most likely end up with a ragged edge along the side of the design where the paint is thicker. I think vinyl decals are a really underrated option. They're super cheap and really, they're so thin most people don't realise it's not painted on. Waterslide decals are the best option if you want the most realistic look (they look printed on) and if you want a more complex design. Here are some examples of what waterslide decals look like - https://imgur.com/a/rXKb4. The toad head on the b button and BMO's face are both waterslides. To add vinyl and watersilde decals to your controller, put them on after you've done two clear coats (and the coats have dried) and then clear coat them again to make them blend in better with the controller (but make sure you wait for waterslide decal to completely dry).

Sparkles

If you want gold, silver, white, black, or holographic sparkles, the best thing to use is metallic flakes. You can get them in different sizes from websites like this - https://www.paintwithpearl.com/shop-custom-paint/metal-flakes/holographic-flakes-prism-flakes/

Please don't buy the sparkles in a spray can. The result are not pretty.

Here's a video of what gold flakes look like on a custom gamecube controller. The video doesn't really capture how sparkly it is, but it still shows it fairly well - https://www.youtube.com/watch?v=i-9VQAjp0uE

If you want sparkles, you'll need to purchase the flakes as well as a clear lacquer and a spray gun (if you don't already have one).

Mix the sparkles and lacquer into the gun and spray as much as you like. Just keep in mind that the bigger the flakes and the more there are, the more clear coats you'll need to add. When I did my sparkly controllers, I honestly probably had to do about 6-7 clear coats before the roughness from the flakes went away.

Joysticks

Don't be afraid to try out new joysticks. Changing out my sticks for xbox one joysticks was one of the best things I ever did. They look super sleek and work just as well, although they do feel a bit different. PS3 joysticks are also an option, but in my opinion look a bit clunkier. Here's what xbox one sticks can look like - https://imgur.com/a/zLAeX. You can also buy glow in the dark ones or metallic xbox one sticks in gold, silver, purple, ect as well as thumbgrips to go on top of the joystick.

If you're worried that changing out your joysticks will affect the way you play, but want the look of different joysticks, I would put a thumbgrip like this one (https://www.amazon.com/GoldenDeal-Silicone-Controller-Replacement-playstation-4/dp/B01AVLVV8M/ref=sr_1_1?ie=UTF8&qid=1476793441&sr=8-1&keywords=thumbgrip+ps3) on your left joystick and then change out the c-stick for a PS3 or xbox one stick and put a matching thumbgrip on top of that (sorry folks, but a thumbgrip won't fit over a normal yellow c-stick, they're too small)

General tips and Things not to do

1. For the love of god, don't try to use a template. Most of the time the paint builds up around the edges and looks horrible. If you want lettering or a design, stick with vinyl and waterslide decals.
2. If the paint gets messed up, wait till it drys before sanding.
3. Make sure the paint is dried before adding another coat of spray paint or a clear coat. If you do it too soon, the paint cracks. Sometimes you can sand out the cracks, but most of the time you're finished and have to discard that controller shell completely.
4. Sanding fixes pretty much everything. Your controller turned into a grave for foolish fly? Sand that bitch out. There's a scratch on your coat from whena blade of grass grazed the paint when it was wet? Sand that bitch out. You put on too thick a coat and the paint dripped? Sand that bitch out. Just make sure you do a light respray after sanding.
5. Be careful if using paper (magazine, newspaper) to spray paint on top of. A lot of times the paper will stick to the clearcoat on the bottom of the controller and massively fuck up the paint job. Use cardboard instead.
6. Don't put a controller back together if you have paint on your hands, even if it's dry paint. Get out the bottle of rubbing alcohol and wipe yourself down, trust me it's not worth the risk.
7. Tape is your friend. If you want to paint the handles a different color than the rest of your controller, blue painters tape is all you need.
8. Glow in the dark paint is crap. Don't fall for their lies.
9. Your buttons will eventually chip if you paint them. Sometimes this takes a year other times it can happen within a few months (melee players I'm looking at you). The safest buttons to paint are the start button, and d-pad and any button you don't use very often (honest to god I don't think I've every used the y button or r trigger). I painted all the buttons on my newest controller and have been using it to play smash for 3 hours a day for the past 3 months. So far the only chips are on the x button. I'm fairly certain this is mostly because I scrap with my nails when short hopping with x, so if you don't have super girly nails like I do then hopefully your paint should last longer. In any case, if you don't use a spray max clear coat, I wouldn't even bother painting your buttons as they won't last more than a few weeks, at least in my experience. I bought a bunch of old buttons and busted $4 controllers from ebay and when I was painting my controller, painted a few extra sets of buttons for replacement. If you're planning on having painted buttons on your controller, I strongly recommend this.
10. Don't spray paint your joysticks. They're rubber. It won't work and you'll end up with a blue thumb.

Edit: Shameless self-plug - I still have a few controllers for sale on my etsy shop at https://www.etsy.com/ca/shop/Crispycontrollers if you wanna check them out.