For Division I - Football Bowl Subdivision (most commonly thought of as College Football around the nation)...
Officially the NCAA does not officially name a National Champion for their Football Bowl Subdivision "FBS" (formerly known as Division I-A). They rely on outside organizations to name a National Champion. Currently that organization is the Bowl Championship Series. The teams with the most BCS National Titles are the Which_NCAA_football_team_has_won_the_most_National_Championships_in_modern_footballof Florida and Louisiana State University (LSU) with two. The BCS has been around for 11 years, so if that is what you would consider "modern era" that is your easy answer.
Other than that, really the only thing you can do is look at All Time National Championships. Before the BCS, there were a plethora of National polls and rankings, so there was no clear national champion every single year before 1998.
As for all time champions... Alabama claims the most all-time with 12. Notre Dame and Michigan both claim 11 andhttp://wiki.answers.com/Q/Which_NCAA_football_team_has_won_the_most_National_Championships_in_modern_football#, Oklahoma, Southern Cal all claim 7.
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