no difference if you are running at stock speeds.
Only disadvantage is if you want to go with more ram in the future, you will have to remove 2 sticks.
Also, DDR2 is pricier than DDR3 right now so you might just want to go with 2x1GB to keep the price down.
$30 for 2x1GB and $52 for 2x2GB for DDR2 800
$24 and $38 for the DDR3 equivalent.
EDIT: I just looked at some G.Skill Ram and the 2x1GB kits that might be the same as yours are $37 and $53 at newegg, http://www.newegg.com/Product/Produc...82E16820231098 http://www.newegg.com/Product/Produc...82E16820231087
I recommend getting the same brand/model of ram for all the slots but if you have the $53 kit, then I would recommend getting a 2x2GB kit so if you need to upgrade to more ram in the future, you don't throw away too much money.
I've been running 4 sticks of ram in my machines for the past 10 years with no issues, and some were mixed brands.