Code:
Gestalt Fighter1/Rogue1 BAB +1 / Fort +2 / Ref +2 / Will +0 | F1 / F1 / R1 / F1&R1
Gestalt Fighter2/Wizard1 BAB +2 / Fort +3 / Ref +2 / Will +2 | F2 / F2 / F2&W1 / W1
Gestalt Fighter3/Cleric1 BAB +3 / Fort +5 / Ref +3 / Will +4 | F3 / C1 / F3 / C1
Gestalt Fighter4/Rogue2 BAB +4 / Fort +6 / Ref +4 / Will +4 | F4&R2 / F4 / R2 / F4&R2
In the above I've put out to the far right what class is giving the "better of the two" at each Gestalt level.
Gestalt 1st
Fighter1/Rogue1 BAB +1 / Fort +2 / Ref +2 / Will +0
Would give good saves of Fort & Reflex adding +2 fort +2 Reflex and Poor Will save adding 0
Gestalt 2nd
Fighter2/Wizard1 BAB +2 / Fort +3 / Ref +2 / Will +2
second Good Fort save would add +1, Being First Good save for Will it would add +2 will, Being first Poor save for Reflex it would Add nothing
Gestalt 3rd
Fighter3/Cleric1 BAB +3 / Fort +3 / Ref +2 / Will +3
Would again Give Good Fort Save, being the 3rd good fort save it would add +0, Would give good Will save from Cleric - This is second Good will save so would give +1, Would be Second Poor Reflex save so no gain
Gestalt 4th
Fighter4/Rogue2 BAB +4 / Fort +4 / Ref +3 / Will +3
Would yet again Give Good fort save so 4th Good fort save would give +1 - Would give Good Reflex save - 2nd Good reflex save so would give +1, Would give Poor Will save - second Poor Will save so no gain
every even Good Save after the first and every 3rd poor save adds +1, Again by RAW you look only at the Progression for save and BAB and HD gains for gestalt. I think people get so caught up in the small parts of gestalt like what actual classes are being emulated by the gestalt class that they try to treat it as a multiclass.
for simplistic try braking it down to just the progression then solve saves as a example
Gestalt Saves
Level BAB Fort Will Refl
1st Fast Good Poor Good
2nd Fast Good Good Poor
3rd Fast Good Good Poor
4th Fast Good Poor Good
5th Fast Good Good Good
6th Medium Good Good Good
7th Medium Good Good Good
8th Medium Good Good Good
__________________________________________
Total BAB -5 Fast BAB 3 Medium = +7
Total Fort -8 Good = +6 Fort
Total Will - 6 good + 2 poor = +5 Will (+5 good +0 poor)
Total Refl - 6 good + 2 poor = +5 Reflex (+5 good +0 poor)
This by the way is
1st Fighter1/Rogue1
2nd Fighter2/Wizard1
3rd Fighter3/Cleric1
4th Fighter4/Rogue2
5th Fighter/Monk
6th Monk/Rogue
7th Monk/Rogue
8th Monk/Wizard
Fort -+6 Reflex +5 Will +5 BAB +7 Flurry of blows BAB +8
The above is all by RAW, I personally Prefer the fraction method, but I assume we are talking about RAW rules.