Hello
Where might I find the cheapest flights from San Francisco to Los Angeles? What about cheap car rentals in the LA area? Thanks!!!

Do you have flexibility to consider alternative airports? At the north, Oakland and San Jose; at the south, Burbank, Long Beach, Ontario?
Southwest Airlines is worth checking (they don't appear on online travel agencies).

Try Jetblue.com from long beach to oakland, across the bay from San Francisco. Southwest.com has the best number of flights, but book early to get the cheapest rate. On southwest, changes are free, but you have to pay the prevailing rate at the time the change is made. Only the higher fares are refundable.

Check Orbitz for flights. See also FAQ post 207: "L.A. to San Francisco Via Public Transit" and FAQ post 148: "Tips on Renting a Car in the U.S. and Driving It Here"

You can see my other posts re: "budget fares" in the US West. The airline is not important - as others above note, the airport and time are the factors that will impact your are. Jetblue and Southwest's fares are not cheaper than full-service airlines - they simply tend to serve secondary airports more frequently.
However, this places a premium on things like car rental, etc., and on average doing things like flying to/from Ontario or Burbank isn't really cost-effective.
Speaking of which, renting cars at LAX is incredibly inexpensive. Consult the usual websites: Orbitz, Travelocity, Hotwire, and Expedia. You should be able to rent a midsize car for around $20/day rental fee, plus another 30% or so in taxes and various extra charges (don't ask, just assume it's coming). I've always found Dollar to have good rates and Honda Accords (if you go fullsize - $27/day recently).
I believe JetBlue flies into Long Beach and Ontario, but not Los Angeles, so unless you have good ground transport, I would pick Southwest or another carrier.

JetBlue flies into Burbank, Ontario and Long Beach from Oakland (will soon start flying out of SFO). Southwest flies from Oakland to LAX, Burbank, Orange County, Ontario. Fares can vary by day and time, so best to check all the major airlines or, at least, Orbitz plus www.jetblue.com and www.southwest.com (since the latter two do not appear on Orbitz, Expedia, etc.).