"1)What certs are co's looking for and are best for a beginner?"
what do you want to do?
CCNA is standard entry-level for networking.
the MCSE and certs leading up to it are standard for Windows stuff.
Red Hat Certified Technician (this is what you want) and Engineer are the standard for Linux.
programming, who knows. Sun has certs for Java, but I don't know who cares about them.
I get the impression nobody cares about the + type certs, except for A+ for entry level..
"2)I was thinking about getting a second degree, are there any reputable online IT degrees out there? Is it worth it?"
the ITground should give you some good online ones.
remember, online schools associated with brick and mortar colleges have more cachet, up to a point.
if you want to go into programming, look for a brick and mortar or online CS degree. Online is hard to find, I think RPI or University of Rochester offers one.
"3)I finished with a 2.9 GPA :( Hypothetically speaking, if I were to put a 3.0 down on my resume would the company check with the school to verify it?"
mildly exaggerate, overbroaden experience, and get creative in listing your accomplishments, up to a point - but never, ever lie.
saying you made 3.0 when you made 2.9 is straight up, verifiable, lying, unless you have a good reason to claim 3.0 (some procedural thing your school does others don't or something). and even then, you need to qualify it by saying you actually got a 2.9.
will companies check? most probably won't. But your resume will be out there with this lie for a very long time.
the head coach of Georgia Tech's football program got offered the top job at Notre Dame, and ended up being rejected in disgrace because some campus reporter, just doing some fact checking, found out about a very old thing on his resume that was false that he put on his resume to get his early jobs.
you should make clear you majored in a hard science - I'd rather have a guy who made 2.9 in physics at any accredited college than someone who made a 4.0 in many accredited psychology programs.