What apps do you mean?
Should I use the custom ROM?
If they found out.. what would happen?
There are many apps that require root access. From some simple screenshot apps to Titanium Backup which will let you backup all your apps and associated data in case you lose something or need to wipe your phone, to delving into custom ROM territory.
I wouldn't tell you that you SHOULD flash th3ory's ROM until you feel comfortable enough with the process.. which will come as you research/read/learn about how to do these things, and additionally you'll probably find someone saying another ROM is more preferable to them, etc... but I believe anyone who's Bionic is running stock (out-of-the-box) would be foolish to NOT flash his ROM if they are rooted.
The current R3BLURR3D version is just amazing... everything runs MUCH smoother and faster than your phone does now, and you'll get a vast improvement in battery life on top of that. Additionally Th3ory and dhacker (the 2 who work on this ROM) have put detailed instructions together which will first allow you to download and install the upcoming OTA (over-the-air) update that Verizon will be releasing to Bionic owners eventually.. which also improves battery life and your radios, giving you a stronger signal and fewer data drops.
Not going to go into everything you'd need to do in detail, but heres some links that will give you an idea of whats involved... just read through and if you have questions, ask. We can advise you, and the developers are extremely patient and helpful with people who are having issues:
The main ROM page itself:
[ROM] [R3]BLURR3D V2.0 PBX MOTO Kernel (10/22/2011) - RootzWiki
This has a bunch of information, videos, tutorials and info about the ROM and about how to get the OTA update (which you should do this before flashing the ROM, but don't NEED to):
[OFFICIAL] Th3ory ROM Bugs and Fixes - RootzWiki
More info on applying the OTA update while keeping root access on your phone:
Forever root + .893 = winning! - xda-developers
[ROOT] R3L3AS3D W/FOR3V3R ROOT V1.0 LINUX/WINDOWS (Get ROOT after 893 OTA OOPS) - RootzWiki
The "ForeverRoot" procedure, as its called, is a quick and easy step you need to do after rooting your phone but before applying the OTA update, because if you don't then you will lose root when you apply the update.
Info on the Cheesecake app, which gets you on the Moto developers' access to getting the OTA update:
*Bootloader Unlock Research* Cheesecake Clarification - xda-developers
Yes... as you can see there is a lot to read and understand before you start messing around haphazardly... but if you feel up to it, its worth it, plain and simple. And its not THAT complicated if you're patient and good at following instructions. The Bionic is my first android phone and I'd never done any of this stuff before, but I've been able to get it all set up and running perfectly without ANY problems by reading and preparing.
Oh some apps you'll need as well (available in the market) are Root Explorer and Bionic Bootstrap. Just get the paid versions, will set you back a few bucks but very worth it, you'll see where they come into play when you start reading.
If you are really interested and have any more questions, feel free to send me a PM with your AIM sn or something and I'll chat with you about it if I'm around, try to clear up whatever questions you got.
EDIT: Oh your last question.. I personally don't use tethering so I can't tell you much about it, there's other threads about how-to and all that stuff. Personally, I would just not bother with it because no one knows yet if Verizon can tell or how they would "punish" people for doing it. None of the things I've recommended to you would get you in trouble doing something you aren't allowed to do. Obviously you'd void your warranty, but thats a risk you have to be willing to take if you're going to jump down this road.