I have used both BSE and IS. BSE on my 2G iPhone, and an IS on my new 3G iPhone. I actually JUST finished installing a BSE on my sister's new 2G, and I put the IS on my new 3G yesterday.
BSE:
- Super cheap & modestly fast shipping (ships in a standard business-size envelope)
- Die-cut is very precise. Quality product
- Same exact material as the IS.
- Took me about 45 minutes to apply. Still waiting for one of the corners to dry a bit... it's being a pain

- >24 hr email only customer service
IS:
- Comes with a squeegie and applicator spray. To be honest, I used my IS squeegie to apply the BSE.
- Die-cut is horribly sloppy. They didn't even remove the camera hole piece or the sim card tray opening... i had to remove those bits myself and slightly stretched my skin (especially around the home button)
- IS covers MORE of the back than the 2G BSE. I don't know what the BSE 3G looks like.
- Doesn't cover the whole front, but it covers what's important
- Lifetime warranty. I went through 3 BSE's (over $25 worth) with my old 2G iPhone... Genius Bar didn't realize I had a faulty SIM

- Phone/email support. Friendly and somewhat knowledgeable staff.
- Took about an hour to install. I screwed up a corner or two.
Overall, depending on the new BSE, I'd go with the BSE. How their site 'looks' is a ****** argument, and I'm a professional web designer. If people love their product, the website shouldn't be the dealbreaker.
Go with the BSE, you'll love it. I bought an IS solely because they had a preorder first, and I was under the impression that it'd arrive before launch day. They effed that up, and as it turns out some people got their BSE sooner than I got my IS via 2-day air. I will not be buying from ZAGG again.