My favorites are:
Lake of Fire (Nirvana)
Sabotage (Beastie Boys)
When I Come Around (Green Day)
What I Like About You (The Romantics)
Ain't No Rest For The Wicked (Cage the Elephant)
Stand By Me (Ben E. King)
It's So Hard To Say Goodbye To Yesterday (Boyz II Men)
The Middle (Jimmy Eat World)
Never There (Cake)
I'm On Fire (Bruce Springsteen)
The Denial Twist (White Stripes)
Bad Moon Rising (CCR)
We Will Rock You (Queen)
You Really Got Me (The Kinks)
Rise (Eddie Vedder)
I agree with many of you that The Beatles, Beach Boys and some other bands have multiple entries. Green Day has few more I could list.
Being The Boneyard I just want to remind folks about song # 4 above which someone made a remix with the lyrics starting "What I like about UConn, they really know how to jam!" this was during the 1989 run with Chris Smith, Nadav, Murray Williams, Scott Burrell, Rod Sellers, John Gwynn, Tate George, Lyman DePriest, et al. That was a wild ride!