I've rooted my phone. Now what? What do I gain from rooting?

Root File Explorers

You can remount your /system/ directory read-write, which will allow you to remove carrier-shipped applications you don't like and so on. Root file explorers can allow you to view all folders on your phone, such as /data/ which is normally protected.

• Root Explorer
• ES File Explorer

Tethering

Some devices already have Wi-Fi tethering out-of-the-box, like the Samsung Galaxy S, so this isn't such a big deal on them unless the carrier charges for the feature.

• Android Wi-Fi Tether
• Wireless Tether

Screenshots

root is needed for screenshots before 4.0-Ice Cream Sandwich.

• ShootMe
• Dropcap2

Backups

• Titanium Backup - Back up all of your applications and data. Also allows you to uninstall system apps, integrate updates into your ROM to save space, and so on.
• ClockworkMod Recovery - Usually requires root to install via ROM Manager. Allows you to backup the entire device, including your ROM, as well as flash new ROMs and other advanced tasks.

Application/Network Control

• AdFree - Removes ads by changing the hosts file (so both ads in apps and in browser)
• Droid Wall - Firewall application. Got an app that's using up all your data when you're not even using it? Block it with this!
• Orbot - Tor app
• Cache Mate - Clear cache of all apps
• Droid VNC Server - Connect to your phone via VNC
• LBE Privacy Guard - Selectively remove permissions from app
• Titanium Backup - Back up all of your applications and data. Also allows you to uninstall or freeze system apps, integrate updates into your ROM to save space, and so on.
• Bloatfreezer - Freeze or remove system apps
• Link2SD - Move (system) applications to a second partition in SD card, liberating loads of free space in /system partition.
• Button Savior - Helps to add on screen button to compensate a failure of a physical button.
• ClockSync - to automatically sync the device's time with few predefined atomic clocks.

USB On The Go features

• StickMount - Automatically mount USB flash drives, keyboards, mouse via USB OTG cable.

CPU Control

• SetCPU - Control the processor speed of the phone, can also setup profiles. It allows underclocking based on conditions, e.g. underclock to 125mhz when screen is turned off. It dramatically increases battery life without affecting performance (when you're actually using apps / the phone) or can improve performance via overclocking.
• Overclock Widget - Similar to SetCPU but less functional

Enable swap file / partition

• ROEHSOFT RAM-EXPANDER (SWAP)
• Memory Swapper Free - support swap file.

Custom Kernels

One popular set of kernels is those provided by ChevyNo1. You can also download them via the premium version of the ROM Manager. Make a nandroid (ClockworkMod) backup before using these kernels! You'll also want to get SetCPU to make the most out of these kernels.

Start with the low voltage kernels at the lowest speed and work your way up to the 1.2ghz. If your phone is stable up to the 1.2ghz range, then try some of the ultra low voltage kernels. If you start getting force closes, then switch back to a low voltage kernel.

Basically each phone (of the same phone brand/model) varies by which kernel it can handle due to the manufacturing differences between processors. So I may have a Motorola Droid that can run ultra low voltage kernels and yours may not be able to run them. These phones weren't necessarily designed to run like this.

Advanced and Miscellaneous

• ROM Manager - Facilitates installing new ROMs with ClockworkMod Recovery, and allows you to back up your entire device (ROM + apps + data) and other advanced tasks.
• Quick Boot - Allows you to reboot into recovery or the bootloader / Download Mode.