Here are some of the searches redone:
Google: 6th
Yahoo: 5th
AltaVista: 30th (now the main site is higher, but these results are still fairly poor)
Ask Jeeves: 4th (not yet updated, the main story is still Jazz 2 Community Junk.)
Fast/AllTheWeb: 12th (not yet updated, but now 12th because another site was moved down. The current headline is Kejero's Tomb Rabbit 2 project.)
Lycos: 11th (also not yet updated, the current headline is Kejero's Tomb Rabbit 2 project.)
Excite: 9th
Hotbot: 38th (large fall, but not yet updated, still on New GBA Article.)
Teoma: 6th (not yet updated, still on Jazz Community Junk.)
CNET Search: NOT FOUND (Still not yet updated, being a metasearch, it may be a while before J2O is crawled.)
Infoseek: NOT FOUND

These are generally really good surprises. I was especially amazed at the jump in returns on Google and Yahoo!, the two most popular search engines. For some reason, it tumbled on Hotbot, but it has not been updated yet and will probably jump when it is. It was found by Excite this time, and 9th is not bad at all. I'm not sure why AltaVista is still finding it so low, even though it has been updated. Infoseek is pay-for-placement, meaning you'd have to pay to be listed at all. CNET Search found it on a search for "Jazz2Online" but not "Jazz Jackrabbit 2". It just may be a while before it updates. It looks like the META tags and header change were sucessful.

And Piccolo: JCF has no popups. Run a spyware scanner. JS.NoClose should not cause popups to just appear out of nowhere. JS.NoClose is a detection of a popup that refuses to close. You should not get these on the JCF. They usually come from unscrupulous sites. However, Ad-Clicker and any other spyware program is a distinct possibility. Ad-Clicker and NoClose are detected by many antivirus programs, but you should download Ad-Aware (http://www.lavasoftusa.com/) for more complete protection.