It is based on a handful of facts combined with the production numbers of each episode. However, instead of cluttering the list with the production numbers, I've decided to list the episodes in order after rearranging them. So, for example, the 3.18 & 3.19 Palm Springs episodes are now 3.14 and 3.15.

Season 3 (covers their 91-92 junior year)

3.1 - The Last Dance
3.2 - The Aftermath
3.3 - The Wicked Stepbrother (Part I) (Dodgers/Mets didn't play in '91 playoffs, but it still implies it's early fall.)
3.4 - The Wicked Stepbrother (Part II)
3.5 - Fake ID's
3.6 - Date Auction
3.7 - Hold Me Tight
3.8 - Home for Christmas (Part I)
3.9 - Home for Christmas (Part II)
3.10 - Love Machine
3.11 - Operation Zack (It's the championship basketball game, so Feb./early Mar. 1992)
3.12 - Cut Day ("25 years ago they cancelled Gilligan's Island" (in 1967), so this episode is in 1992)
3.13 - SAT's (This episode could be in fall '91 or spring '92, though Junior SAT's are usually in the spring)
3.14 - Palm Springs Weekend (Part I)
3.15 - Palm Springs Weekend (Part II)
3.16 - Check Your Mate
3.17 - Pipe Dreams
3.18 - No Hope with Dope
3.19 - Rockumentary
3.20 - Mystery Weekend
3.21 - All in the Mall (U2 didn't play any dates in 1991 when this episode aired, but they did play a handful of dates in California in April '92.)

The pre-Malibu Sands part of season 3 is tricky to order without redundancy. There are 3 two-parters, therefore, I tried to space them out. I also believe the final 3 episodes listed above could be ignored altogether.

The Malibu Sands (pre-senior year summer)

3.22 - Zack's Birthday
3.23 - The Game
3.24 - Fourth of July
3.25 - Boss Lady
3.26 - My Boyfriend's Back
3.27 - The Last Weekend

Season 4 (covers their 92-93 senior year) (No Tori eps.)

4.1 - Best Summer of My Life (Zack says it's the first week of school)
4.2 - The Fight (Zack introduces their senior year at the beginning)
4.3 - The Bayside Triangle
4.4 - Wrestling with the Future (Mentions Lisa getting into the Fashion Institute from "Bayside Triangle")
4.5 - Student-Teacher Week
4.6 - The Teacher's Strike (Zack/Slater skiing at Big Bear Mountain implies that it's winter)
4.7 - Screech's Spaghetti Sauce (Belding mentions a new term; could go before The Senior Prom, too)
4.8 - Isn't It Romantic? (Occurs on Valentine's Day, meaning it's still winter)
4.9 - The Senior Prom
4.10 - Graduation
4.11 - The Time Capsule

Season 4 is short without the Tori episodes, but having them mixed in with Kelly/Jessie eps. is strange. There is no explanation for why they disappear.