From what I'm hearing, the ending of season 4 ties this season into all the previous seasons.
We don't know if Palmer is good or bad. He seems to be good and seems to be extraordinarily ethical, but he has his utilitarian streaks... ordering the death of a government agent (military, I think, since CTU seems to be a DoD organization with a chain of command) to prevent possible terrorist retaliation in Season 3.
Here's an ultra-short summary. There are a million subplots, and I've undoubtedly left out some important ones.
---PREVIOUS SEASON SPOILERS---
S1: It's the day of the California presidential primary; Senator Palmer is running for president. Some Serbs are upset at Jack and Palmer; Jack was part of a special ops mission into Belgrade to kill Victor Drazen, and Palmer was head of the Senate intelligence subcommittee that authorized the mission. Unfortunately, Victor Drazen wasn't killed, but his wife and daughter were. His two sons have orchestrated an elaborate scheme to kill Bauer, Palmer, both of their families, and to free their father who was later captured by the DoD and has been held unofficially ever since. Meanwhile, Nina Meyers, Jack's second in command and ex-lover, is really a freelance terrorist/infiltrator who for the moment is being instructed by her employers to feed the Drazens information. We also find out that Sherry Palmer is pure evil, and the senator separates with her at the end. Also at the end, Jack kills Victor Drazen and his last living son, so they're out of the running for evil masterminds in later seasons. Nina also kills Jack's wife, the discovery of which is the last scene of the season.
S2: Palmer is now president. Some terrorist group is going to blow up a nuclear bomb in Los Angeles. That terrorist group is connected with a certain unnamed middle-eastern country, except it's not. The recording linking the terrorist ringleader with the leaders of several countries was fabricated by an audio genius, and Jack has to get the evidence before VP Prescott launches a retaliatory attack on the "responsible" countries (Palmer gets kicked out of office via cabinet vote on the incapacitation clause of the 25th amendment.) It turns out there are two evil ringleaders, "Max" and Alexander Trepkos, and their go-to guy, Peter Kingsley (who Jack kills at the end), who want a war with the middle east so their oil holdings go up in value. At the end, we hear Max tell Trepkos that "we'll have to do this another way." Sherry Palmer is partially involved in this, but presumably isn't prosecuted because she helps entrap Kingsley at the end, which allows Jack and CTU to save the world.
S3: All 5 other members of Jack's team on the Drazen mission, called Operation Nightfall, were supposedly killed in an explosion. Well, one wasn't: Stephen Saunders, a British operative (SAS or something), and he claims to be upset at the U.S. because of its interventionist foreign policy. He gets a lethal virus from someone who scammed Jack and some drug dealers (there's a major subplot here that I'm leaving out) on his way to deliver it to Saunders, and Saunders threatens to release it bit by bit unless President Palmer does what he's told. Saunders is stopped before he gets around to his main request, but he succeeds in getting Palmer to say "The sky is falling" in a press conference, and also successfully requests that the regional director of CTU, Ryan Chappelle, be killed. Nina was involved in the drug dealer subplot, but Jack kills her soon after she's brought back to CTU for questioning.
There's also this mysterious freelance terrorist named Mandy who blew up a plane at the beginning of season 1, and also nearly killed Palmer with some sort of poison at the end of season 2 at Max's behest. It's unclear so far what the attempt on Palmer's life is supposed to accomplish.