Is this a matter of unique and creative super powers, or super powers that are up for grabs to use in your story?
If it's the former, I think you will get a long line of those from other people. Therefore, I will talk a little about the latter and might give a few suggestions of the unique and creative department in later posts.
For powers that are up for grabs, for the most part you could look at the parallel/equivalent characters across both Marvel and DC. For instance, "the flash" and "quicksilver" both having super speed means superspeed becomes something of a "free use" power any person writing super hero comics can use.
On the other hand, Spiderman is a power that only exists in the Marvel universe. Therefore, a super hero with spider powers is absolutely NOT up for grabs. (There are also some that appear from Hanna Barbara cartoons. Those ones are DEFINITELY up for grabs.)
Going by this standard, the stock list of powers would be...
Super strength. (various)
Super speed. (flash and quicksilver)
Flight (various)
Eye lasers (various)
Solar powered heroes (Superman and Birdman)
Special opps combat training (Deathsroke, Punisher, and Deadpool)
Ninja training (Various including Batman)
Assassin training (Various including Batman) (Yes, ninjas and assassins are different, although there's some overlap)
Magic power in superhero world (Dr. Strange and Zatana)
Technology based ice powers (Dr. Freeze and Captain cold)
Possessing physical wings (Hawk man/woman and Birdman)
There are also a few others that, despite only really existing on one side of the marvel-DC line, are otherwise generic enough to be used anywhere anyway. However, since they only exist on one side of the line, you have to be a little more careful handling them not to have them look too much like the origin that has been used by one of the bigs. You gotta modify it just enough to seem disimilar.
Techno suits (Iron man)
Control of plants (Poison Ivey)
Drug-based super strength (Bane)
Healing factor (Wolverine and Deadpool.)
Flame powers (Human torch and... I forget the X-men character's name)
Ability-based ice powers (Iceman from X-men)
Psychic communication (Dr Xavier)
Telekenisis (Gene Grey)
Ability steal (Rogue)
Teleportation (Nightcrawler)
You might notice a pattern here. Most of these powers are from the X-men franchise. This is because X-men used a large assortment of simple powers without stringing them together into a complex origin story aside from this X-gene. For the most part, with the exception of some very specific powers like Magneto or Apocolypse (mostly it's the villain powers from X-men you gotta stay away from,) the majority of the X-men powers are up for grabs. Also, Cyclopse's eye-beams are already listed in the cross-over as being up for grabs, but using his specific application where he can't turn it off and needs the visor in order to hold it in is DEFINITELY out.
There are also a few power sets that appear in both Marvel and DC that, despite them appearing in both, are also specific enough in theme that they cannot be used. An example of this would be Spawn and Ghostrider. The "rider of the damned" theme is something you should probably stay away from for liability and copyright reasons.
There are also a few powers that are not so attached to the big names that are just generically used in a lot of the more cheap knock-off super hero themes. These are ideas that you CAN use if you are so inclined, but I would recommend avoiding none the less due to their association with cheap themes.
Super intelligence.
Wrist-band lasers
Laser guns
Ok, that's actually the list. There are several other powers I've seen in those cheap-feeling superhero programs, but those ones are the only ones I have seen that ONLY appear among the cheap knock-off superheroes. Most of the other powers that appear in those settings are powers I've also seen well done in other areas, such as stretching/elastic powers.