Caped, you may well regret having asked me for this list since it also brought up some ideas for other feature requests to go with it.
But here goes, as I may as wll get this posted before the hitman comes to get me...
I would recommend a User Activated effect for the following:
Edges
Champion- +2 Toughness (+2 damage as well but I'm not sure there is a way to add that globally) agaisnt supernatural.
Double Shot (FC) - -2 Shooting for the attack using this. Arguably this is for Bow only but I don't think checking for that is particularly important. The Improved version doesn't need a checkbox since it just removes this -2, so they just wouldn't bother checking the box.
Exorcist (HC) - +4 opposed Spirit and Faith test -v- deamos/supernatural evil. Somewhat specific but it could be for extended tests so may well be worthwhile to include, IMHO.
Frenzy - I'm torn on this one, but for a Frenzy fighter they may well do this constantly, so should probably have a checkbox for the -2 Fighting penalty. (Improved removes the penalty so no need for anything there.)
Giant Killer - This one would require adding a +1d6 bonus to all the damage values on the sheet if checked. Not sure if that is even doable, really.
Investigator - Add the selection for the +2 Notice part only (when searching through evidence). Although that one may not be all that common.
Liquid Courage - Vigor +1 die and ignore one wound level modifier. There is a further effect if fully inebriated (-2 Smarts and Agility) but I assume there is no way to have two activation boxes.
Marksman - +2 Shooting and Throwing (only when no movement during the round and RoF 1 is used.)
One of the chosen +1 (HC) - +1 to Fighting, Shooting, Throwing, and any arcane skill (but only vs. supernatrual Evil).Text needs to be fixed to remove "either" from the first sentence.
Sunder (FC) - This one might not really be possible, adding AP 1 to all weapons when check
Hindrances
Allergy (SPC) - -2/-4 penalty to all rolls when exposed.
Blind - -6 to everything when selected. Although it is only for "physical tasks" if you really wanted to go through the list and determine what is and is not physical. If you do that, though, then it's also -2 to "social" tasks (so Persuasion, Streetwise, and Intimidate, presumably.
Doubting Thomas - -2 Guts (only for supernatural horrors). This might be a candidate for not doing it, but with some settings it could be pretty common.
Hard of Hearing (Minor) - -2 Notice for hearing checks only.
Phobia - -2/-4 to all Trait rolls when in the presence of the Phobia.
Terminally Ill (SPC) - -1 to all Trait rolls for a session.
Some of the following could potentially have such an effect but I'm not sure it's worth adding it because the situation it arises in is probably fairly rare.
Edges
Arcane Resistance and Improved Arc. Res. - +2 to all opposed rolls and +2 Armor (toughness) against arcane powers. That one may come up with some regularity but in a very piecemeal fashion (arcane this attack, mundane for these 4 others, etc.) I think it's best to leave this to the player to just remember. Although if you've got a big Mage Battle type of campaign I supposed it could be useful.
Brave - could add a selectable +2 to Spirit, but Fear checks are usually 1 shot rolls, not something you're making over and over again that you might need a reminder for it.
Counterattack - -2 Fighting is a very specific circumstance so I think this is also not a good candidate.
Mentalist - Same as Arcane Resistance but with the Psionics skill specifically, so I think this one is also probably not a good candidate (although maybe for a Psionic heavy campaign with lots of Psionic battles it could be useful?)
Quick Draw - Also seems to be a one-and-done roll, so probably doesn't need this.
Strong Willed - To add a checkbox only for the +2 Spirit and Smarts rolls when resisting Test of Wills. Pretty specific situation, but I suppose it might be worth adding for a campaign where Tests come up a LOT or something.
Sweep - -2 Fighting... might be worth having a checkbox for with a Fighter that does it a lot?
Tower of Will (HC) - Same comment as for Mentalist. I can see an argument being made to include this one, but I'm not sure if it's really worth it to do so.
Several others affect rolls for Shaken or Soak that I think probably just don't come up enough to justify adding a checkbox for them.
Hindrances
Anemic - -2 to Vigor but only for Fatigue checks, poison, disease, and the like, which may well be staggered among other standard Vigor rolls and the like, so probably not a good candidate for coding in.
EDIT: These have been added in v2.7