You can get programs such as "xbackup" that will backup all your jailbreak/cydia settings with your itunes backup. There's a few downsides. If you heavily customize your phone with custom shit in winterboard, swap icon and UI images, etc, then that doesn't backup and will all need redone, which can be a pain in the ass. My phone is pretty heavily modded visually, so I don't update often. I started with 4.0.1 and didn't update til 4.3.1. I guess another downside is waiting for a stable jailbreak release. So even if they do release IOS 5, you may have to wait a few weeks to update it if you want to stay jailbroken.
With that said, those are minor inconveniences, or at least to me they are. The benefits far outweigh the inconveniences.
XI Wiki


