Bone stock will always be worth the least amount for this car. By that I don't mean that a modified car is worth more....
My logic to this comment is specific to there being a couple of 'stock' Achilles heel items. Specifically the DRC and the transmission. These are two big $ items that unless than have been replaced will guaranteed become a cost impact item. If the DRC has been replaced for the Gen II version you're better off than stock, but still at a potential risk depending on you 'luck'. Coil overs have been noted by many as being the only suitable replacement and there is lots of opinion about whether or not they are better or worse as a result. Transmission replacement will ensure you get suitable resale value as the person buying has plenty of visibility to the woes owners with this car have with stock transmissions. A replaced transmission doesn't mean it's modified/hopped up, it merely means it's dealt with the flaw in the original design - just like that of the Gen II DRC.
Now, if you go one level more and get in to after market modifications then you could certainly look to argue some make the car worth more - although many here would be quick to debate whether that is in fact accurate.
To consider:
Tune - no added value
Rims/tires - limited added value if any
RSNE - Some minor added value
Preventative maintenance items with recent work - i.e. rotors/pads, axles, waterpump, timing belt, T-stat, etc - Added value since they will be a cost anyway
Exhaust - added value
Piggies - added value
Turbos - added value