Some Utilities and System mods are the first reason to jailbreak. SBSettings is essential to quickly and freely setup main options, perform basic actions, ssh, springflash, and even take notes within an app. Remove BG will save you the pain of having to close all apps by hand - and you can except apps you know you usually want to remain open. Zephyr will add multitasking with simplicity - but take the time to set options correctly or it's a nightmare. SMS counter is cool when you want to keep the high hand on your usage. And so on...
Then theming, of course. Customizing without excess is my way. Define excess... well like others mentionned I'm quite OCD about the looks. It has to be neat. I saw many awesome complete themes... fabulous creations, really, and neat in their original ways... but I like the basic look of the native apps icons, that's my kind of neat. Love the stock apple in many ways, so I only choose what is often the most simplistic way to add a customizing option the native iOS doesn't allow, but should. Adding one column and one row, plus five icons dock, is always my first mod when I'm done jailbreaking a new device. My Status Bar might be a tad more expressive, but nothing much, really.
But the best is when one meets another in the creation of a function you just love, with killer looks. Such as combining FolderEnhancer with GridLock and a couple of font/color changes. If you'll allow...

Starting with the basic homescreen, where we can see that an icon label misses its icon... that's my folder. Named it accordingly to wallpaper. Then you can (not really) see my folders in the folder... then a peek into one of the folders that's got apps directly in it.
Other folders open more folders... I kept the folder labels because it's mostly for fun and I want to keep my use simple. But you can remove them too... and then create a maze of invisible and randomly placed folders in folder to hide private things...
And I like to have all in one page that seems to contain nothing, except that which I use all the times.