An excellent idea - I'm a big fan of the show, but I never connected the dots about adapting the show into the d20 system. You both have a point though: both d20 Modern and Spycraft would probably be a good base for the setting, and each would be probably play differently.
My Spycraft books are on the way, so I'm just going on things I heard in reviews, and my knowledge of what d20 Modern will be like is pretty basic
In the below, I'll just stick with Spycraft for now until d20 Modern comes out (all of the Spycraft specific information listed below was swiped off reviews from RPG.net)
"Races":
Player Races: human (default), Jaffa template*, various others
Non-Player Races: Goa'uld template*, Tok'ra template*, Asgard**
*templates could either be balanced with advantages and disadvantages, or certain templates can be ECL (I have no idea if ECL exist in Spycraft).
**Since Jaffa, Goau'ld and Tok'ra are all based on "Humans", I'm not sure if Asgard and other non-human related races need to be more "above and beyond".
"departments": not sure which classes are totally inappropriate, and if any new ones need to be created specifically for Stargate. Perhaps just a rename and a few tweaks.
- Home Office: not appropriate?
- Power Brokerage: command/politician
- Military Operations: standard background
- Computer Espionage: make more technical related, in general?
- Urban assault: Special Ops?
- Black Ops: ???
- Wetworks: ???
- "The Basement": shoehorned for "Academic" or does that need to be separate?
"Class": not sure which classes are totally inappropriate, and if any new ones need to be created specifically for Stargate. Perhaps just a rename or a few tweaks.
- Faceman: modified diplomat/command functions?, Undercover?
- Fixer: ???
- Pointman: ???
- Snoops: modified to be technical in nature (beyind just computers?)
- Soldiers: as is?
- Wheelman: modified to incorporate piloting (aircraft) skills?
Again, an academic related class is missing and I'm not sure if any of the above can be showhorned into this role.
Skills: Stargate specific skills? (probably modified Knowledge, Craft, etc. skills)
tbd
Feats: Stargate specific feats?
tbd
Items to take into account aka will need rules for them(taken from
www.stargate-sg1.com):
- the Stargate: uses 6 of 38 symbols, representing star constellations, to locate another Stargate and then uses a final 7th symbol, unique to each Stargate, as its point of origin. However, the Stargate contains nine chevrons.
- The Iris
- Naquada: a quartzite metal not found on earth which the stargate is composed of
- G.D.O. (Garage Door Opener): a small transmitter capable of sending a coded signal through the gate
- F.R.E.D. (Field Remote Expeditionary Device): carries supplies for field units on the other side of the Stargate. With six wheels, FRED can navigate almost any terrain.
- M.A.L.P. (Mobile Analytic Laboratory Probe): travels through the Stargate to unexplored offworld locations, determining whether or not it is safe for human teams to proceed through the Stargate.
- D.H.D. (Dial Home Device): activates the Stargate.
- T.E.R. (Transphase Eradication Rod): detects objects operating in the light spectrum 180 degrees out of phase of human vision, like the alien race the Reetouh.
I'm not exactly sure what this item is 
- various Goa'uld weapons (staff weapon, "zat" (sp?), etc.), equipment (the hand healing device, etc), vehicles (motherships, deathgliders, etc.)
Other (taken from
www.stargate-sg1.com):
Special SG team designations:
SG-3 - Marine combat unit, lead by Colonel Makepeace.
SG-5 - Marine combat unit.
SG-7 - Scientific Corp.
SG-8 - Medical team.
SG-9 - Diplomatic Corp., led by attorney Major Stan Kovachek.
SG-11 - Engineering Corp.
Creatures:
- Replicators (various sizes)
Just threw the above up for now: no time to watch every episode and read every episode synopsis just yet
)... hmm...
