LOL, how about a special weapon for the Intrepid Class? Hazard Team!!! That could own!  

i find it annoying when borg beam over to MY ships when the sheilds are down but MY ships don't board derelict ships whether friendly or enemy! i want to capture my enemy's ships!

lol @ the black baron's "who the **** can take over a cube?"

i would like to see the borg without shields as its more...hmm whats the word....always bandied about never understood it....CANON! thats it its more canon!  

Cpt Ryan is right, the borg transported to the EE right before their sphere was blown to bits by the quantum torpedos fired AFTER going through the temporal distortion or whatever it was. There are "combat windows" in shields which allow friendly ships with the proper codes to transport through shields, send communications, receive sensor info, etc.  

The simple as is the Federation's policy wouldn't be enthuthiastic of stealing enemy craft. Unlike in one of the Ds9 episodes where Sisko finds an abandoned Dominion fighter, he comments on how if it was theirs and if someone was there to say it was theirs, he would've left it...but that's by the by.

And who could take over a Cube...I'm guessing Species 8472 could. It didn't take many of their ships to disable a whole squadron of Cubes now did it? (Scorpion Pt. 1)

We do know though that the Borg have some sort of shielding. In BoBW pt. 2 when Data and Worf rescue/kidnapp Picard/Locutus they get through a "barrier". This will undoubtedly protect the ship from some sort of weapons damage before it get's thgouh to the hull.