Clem had a question in the Suggestion Pot :
Supers gaming: In a world with ubiquitous security cameras, DNA analysis that can identify someone from a skin cell scraped from their knuckle by an evildoer’s five o’clock shadow, image and profile matching software, huge fingerprint and medical ID databases, easy wiretapping and bugging etc.; how does an enterprising vigilante protect his/her/their/its secret identity?
I just finished an interesting book, Superpowers  by David J. Schwartz. A lot of the book has to do with the difficulty in keeping a secret identity. It is set in the Summer of 2001, when a lot of today’s investigative technology exists, but before the widespread popularity of CSI and some of the more recent changes to information gathering law and practice.
The shallowest answer is to hand wave it away as not a problem. Just as Clark Kent’s glasses are enough to throw everyone off, maybe no one thinks to use technology to unmask the heroes. This will work in a game until someone brings it up… then it will feel like a plot hole. A way to counter this is to explicitly discuss secret identities before the game; if everyone agrees that they want secret identities to be generally effective and that it’s not an interesting complication to deal with, then you’re set. For specific plots you can reverse this, but the underlying assumption is that it’ll basically work and no one will look too closely.
A variation of the shallow answer is to just define the PCs as unidentifiable. If the PCs share a common origin (like magic or mutation), a side effect of their condition might destroy their identifying markers. Maybe one of the PCs has an ultra violet blast that sanitizes the fight scenes, or the mage knows a cantrip similar to Shadowrun’s sanitize spell that instantly cleans the scene of hair, blood, and other common identifiers.
Another option is to use realistic science, but bend things in favor of the PCs keeping their identities. Use those depressing newspaper stories about contaminated crime labs, mixed up bloodwork, and laboratory funding cuts, to explain away the researchers failure to break the IDs. Realistic limits might mean that they only have time to identify a couple of common genetic markers instead of sequencing the PC’s whole genome, that the fingerprints are taken and compared to paper records… there’s no money to computerize everything. Or that the partial prints have 11,000 “potential hits” and no one is willing to do the drudge work when there are more important crimes to solve. You can go so far as to play this for laughs; one week the intrepid reporter notes that one of the heroes has dog genes in their DNA (thanks to sloppy blood gathering), the next week she reports that “eye witness reports place the vigilante as a while male 5′-8″ to 6′-2″ tall”, the third week her expose reveals a 0.12% chance that the masked crusader is related to the Hapsburg line.
If secret identities are important, then maybe it’s time for the PCs to stack the deck. A friend in the crime lab can explain why the blood samples are never pure enough for analysis. It works for Nick Knight — why not find your PC a Natalie? Someone on the supernatural investigations division of the local police might make for a good contact/DNPC. Take advantage of the fact that the PC needs something from the NPC and make it a dynamic relationship. Do you want to stand up the only person who can lose your DNA sample because you have another dinner scheduled?
PC skills and powers can provide good backstory reasons for the security of their secret IDs. A computer hacker character could have a virus lodged deep in the FBI that deletes any fingerprints or other identifying characteristics for the PCs. A shapeshifter might shift finger prints whenever they change forms. Special gloves might be a side effect of one PC’s genius, or Lancelot dresses up in plate armor in the 21st century just to prevent those blood splatter problems. Who knows what damage is done to hair and blood when they pass through a force field?
If you enjoy the idea of beating security systems as a major subplot, mention that you’ll use realistic surveillance and crime scene technology during character generation. Knowing that they’ll have to deal with realistic snooping might alter their choices about techniques and tools. Little Brother X  is a great novel that deals with modern surveillance and keeping your identity concealed. Beating the surveillance state might provide an interesting constraint on their actions; like Marcus, they’ll have a handful of pebbles on hand to alter their gait when it’s necessary.
Those are some of the solutions I see for Clem and his group. Do you see some good ideas I missed? What flaws are there in the things I suggested? Could you keep a secret ID if you allowed the NPCs to have the supertech of comic books and CSI?