Spikes' deal is for three years, Clary's is for four years and McMichael got a one-year deal.
Safety Bob Sanders previously agreed to a one-year contract.
The players' contracts are expected to be signed on Friday.
"All four players are veterans and have performed at an extremely high level," coach Norv Turner said. "Obviously Jeromey has put a lot of work in with us to get to where he is and we're excited to have him back. The continuity of keeping the offensive line together is big.
"I think defensively you want to be as strong as you can be down the middle and with Spikes and then Sanders, you've got two strong personalities that bring a real aggressive presence to the defense."
A hard-hitting, veteran entering his 14th season, Spikes got a call from general manager A.J. Smith on Tuesday morning, when teams were allowed to negotiate with free agents.
"He is an outstanding player. Takeo will bring his physical, aggressive style to our defense," Smith said. "I love his competitiveness and instincts. I believe he will be an immediate contributor."
A two-time Pro Bowl and All-Pro selection, Spikes played inside linebacker for San Francisco the past three years in the 3-4 scheme under Chargers defensive coordinator Greg Manusky. Spikes has also played for the Eagles, Bills and Bengals.
Sanders is a former Defensive Player of the Year with the Indianapolis Colts, earning Pro Bowl selections in 2005 and 2007. He had a torn biceps last season on Sept. 12 at Houston and missed the rest of the season.
Clary has started 42 regular season games for San Diego the past three years.
"I'm extremely happy that I get to stay here in San Diego with the guys I've worked so hard with the last five years and continue to build and get better and work our way to a Super Bowl," Clary said.
"Just from a work ethic standpoint, he's a guy that can't be matched," Chargers center Nick Hardwick. "I've tried to keep up with him working-wise and I just can't do it. He's a big piece, to show guys how to work."
McMichael, a 10-year veteran, caught 20 passes for 221 yards and two touchdowns last season, his first with San Diego.