I don't know that I think any are better at night (except maybe the teacups), but most of the outdoor rides are a different experience at night and can seem like a different ride, especially the ships of RoA, Storybook Land (double especially during the holidays with the little Christmas decorations), Jungle Cruise, and Golden Zephyr.
Although, if you can time it right, my favorite time to ride California Screamin' is just after the sun sets when all the lights in and around the parks are on but it is not yet too dark to see the buildings and landscape.
Big Thunder Mountan Railroad: it's mad fun because you don't really have a sense of where the drops, turns, and tunnels are compared to the daytime. It's just so much more thrilling and provides such a different experience.
Matterhorn Bobsleds: if you're willing to miss out on catching a spot in front of Sleeping Beauty Castle for the fireworks, it's definently a must ride! Ride it when the fireworks are going off because when you get to the parts of the ride where you're lead out of the mountain, the view of the fireworks is amazing! Even without the fireworks, the ride is still more thrilling in the dark night. Roller coasters at night are ten times better, well in my opinion.
California Screamin': It's sort of hard to get on this ride at night now because of World of Color, but if you get the chance, the ride is much more breathtaking. The pier all lit up at night I think is what makes the ride ten times better. Paradise Pier is just amazing at night.
Besides the ones previously mentioned, the Jungle Cruise. Autopia is fun at night too. The outdoor portion of IaSW is beautiful at night. I almost never ride it, but the tea cups look nice with the lanterns hanging above.
In the category of no longer around, the PeopleMover and Skyway were GREAT at night. Oh, and the Rocket Rods.
Count me among those who love BTMRR at night. That's a fun one for sure - the overall feel is just much different. Space Mountain is...well, you can see more at night because your eyes are better adjusted, and that's not a good thing, but the lighting outside really sets the tone nicely.
In a much different vein, the Jungle Cruise takes on a nice sort of peacefulness at night. So does the railroad.
The matterhorn, especially the fantasyland side is a much different, more thrilling ride at night. I couldn't imagine riding the jungle cruise NOT at night, but that's just how I've always ridden it. I also prefer haunted mansion and tower of terror at night just for the ambiance.
I also have to completely agree with Strider GX35, nothing beats just walking down Main St at night.
Thunder Mountain and Matterhorn are both excellent rides for the night time. Haunted Mansion and Pirates are also great rides at night when your eyes are already dark adapted.
Our revels now are ended. These our actors, As I foretold you, were all spirits and Are melted into air, into thin air: And, like the baseless fabric of this vision, The cloud-capp'd towers, the gorgeous palaces, The solemn temples, the great globe itself, Yea, all which it inherit, shall dissolve And, like this insubstantial pageant faded, Leave not a rack behind. We are such stuff As dreams are made on, and our little life Is rounded with a sleep. mycroft16 on Twitter
Jungle Cruise- It's very peaceful, yet more dark and mysterious. The animatronics look a little bit more realistic too. The skippers can be tired around this time, but I once had one who took their spiel to the next level (At night) and made it one of the best Jungle Cruise experiences I've ever had. This is excellent theming on Disney's part, you really feel like you're in the jungle. Adventureland in general is really cool at night, as are New Orleans Square and Main Street.
Indiana Jones Adventure- The queue is extremely dark (Not extremely) and pretty ambient. The indoor portion of the queue is even better at night as no daylight pours in. When you exit and pass the Jungle Cruise you can see part of the Cambodian Ruins. The sounds of the jungle are coming from all around you which contribute to making you feel like you're in the jungle. To make that even better you can hear the rumbling of a far away boat (Very relaxing to me), and when no boat is passing, it's so dark you feel like you're lost in the wilderness. I could seriously die there if I wanted to.
Haunted Mansion (And Haunted Mansion Holiday)- All together better at night for me.
It's a Small World (And It's a Small World Holiday)- Entering at dark and exiting at dark (From within the show building) is always fun for me.
Roger Rabbit's Car Toon Spin- Good memories getting lost in Toontown at night (Of course before the fireworks).
Space Mountain- Exiting at night is pretty fun.
Finding Nemo Submarine Voyage- All the underwater lights you can see from outside the lagoon make me feel like I'm home for some reason.