• Think of itch.io as a place to host your game for free. They have nice widgets that can embed into your website for an easy "cart checkout" experience. GameJolt is more of a platform similar to Steam. They have trophies (achievements) integration, leaderboards, and user-only and game-wide cloud storage service (think Cloud Saves on Steam, as well as trading in-game items with other players of that game, etc).
• In itch.io you follow the game's developer. On GameJolt, you follow the game itself.
• You can rate a game even if you haven't played it in itch.io. On GameJolt, you need to have launched the game one way or another before you can rate it. The difference is that, rating is less prominently displayed on itch.io than on GameJolt. On GameJolt it is directly visible up top, on itch.io, you have to click on an expando link to view it as well as other info like when it was uploaded, the game's tags, etc.
• In addition to showcasing your videos/screenshots, game pages in itch.io allow you to upload your own background image as well as pick the color scheme and choose from a handful of fonts. It's the same case when it comes to your user page where you showcase your games, you get to customize it up to a certain degree only. GameJolt has a more uniform-looking game page but they've introduced Custom Game Sites & Portfolios which allows you to upload a static website both for your games and for your user page (portfolio) so it allows far more customizability.
• Both of them have desktop clients to help with keeping your game library on each platform organized and easy to update. However, I found that GameJolt's client has been outdated for some time now. (last update was August 3, 2016) It has a lot of missing quality-of-life features. I asked before and they said an update was coming soon-ish but I guess seeing as there hasn't been an updated still, that it has been moved to the back burner again. However, itch.io's client is pretty much a glorified browser. If you have multiple accounts hooked up to it, you can swap between them and keep your cookies and tabs intact for each account. There's a userscript that adds the ability to open game pages on the client kinda like how Steam does. It makes it easier instead of having to copy+paste the URL from the browser to the client. GameJolt doesn't have this leisure as far as I know. You have to search for the game manually on the client. The itch.io client allows a supposedly safer sandboxed environment so even if you download a malware pretending to be a game, the damage would be minimal. GameJolt client doesn't have this but then again, so Steam doesn't either AFAIK.
• It's easy to set up a merchant account on itch.io, you just provide your PayPal and that's it. On GameJolt, I'm not sure but if you live outside the supported countries, you have to fill out a Google Form and wait in line while they go through it and approve/decline them manually (which takes a long time if what I see on complaints are true). They only support like 2 Asian countries so if you live in Asia, get ready to wait if you want to sell your games.
• In monetization, both itch.io and GameJolt lets you set a baseline price for your games and people have the option of paying more if they think you deserve more. GameJolt also has the option of sharing ad revenue as another monetization method while itch.io doesn't have that.
• You can use Bitcoin, Credit Card, and PayPal to make purchases on itch.io, on GameJolt, you can only use Credit Card and PayPal.
• Design-wise, I honestly prefer GameJolt's look more as it looks more polished and clean whereas itch.io's look more basic. But that's just me I guess.
• Added by yaru, GameJolt focuses only on games whereas itch.io caters to not just games but other things too like game assets, tools, eBooks, and the like.

These are the things I observed using both platforms.

Well, thank you for your detailed answer. I feel more informed now.

Hmm, you neglected to mention what I personally think is the most important difference... GameJolt is 100% about games, Itchio lets you sell stuff like game assets, digital books, and even physical goods. So itchio basically is a marketplace for everything, so all kinds of indies can use it, not just indie game developers. AFAIK it's pretty much the first place that does this in the west, which is really cool~

(and yeah, I'm a bit biased here since I do game assets more than I do games nowadays... sorry about that :P)

Also, having used both: Itchio is much easier to use - it feels like every workflow and menu in GameJolt has a few extraneous steps added for no apparent reason, and you basically need to have a guide open in another tab to get ANYTHING done because a lot of stuff is so obtuse. Itchio not only has easier steps for everything, most of them are optional.