I've looked at reasons for keeping or blowing the base.
I have 3 main charactera- A Paragon, a Renegade and a more neutral guy (a mix).
I blew it with my Para, kept it with my renegade, and so with my neutral guy I had to choose...
I went with keeping it. I checked a few of the arguments against keeping the base and examined them:
1). A point a lot of people make is that the base could indoctrinate and corrupt any cerberus team experimenting there- similar to what happened to the derelict reaper. This indoctrination could be caused by reaper technology implanted around the base. While this is a fair point, I realised a few things which undermined the validity of this argument. Firstly the base contains collectors. As they have been implanted with cybernetics and modified genetically, the reapers don't need to have equipment to indoctrinate them- they don't need indoctrination! However what if the reapers have indoctrination devices as a means of defending the base should it be taken from the collectors? Again, unlikely- the Omega 4 relay debris field as well as the legions of collectors meant that losing the base was highly unlikely- I'm going to take a leap of faith and assume that the Reapers did not expect the base to be taken and thus didn't take the necessary precautions of laying indoctrination devices in the base.
2). Another argument was that humanity should not dabble in technology that is way beyond their time. Looking at the effect of the Salarians giving tech to the Krogan (thus inevitably triggering the Krogan rebellions) this argument appears valid. However keeping the base wouldn't be the first time humanity have used reaper/collector technology: Okeer made deals with the collectors in order to further his plans of creating a Krogan super soldier- thus Grunt was made partly through the use of collector tech. Grunt was a valuable asset to the team and didn't end up screwing things up. The Thanix cannon is also based on advanced reaper tech, again this was a valuable piece of technology- it helped wreck the collector cruiser. Even EDI was based on reaper tech! If it weren't for EDI, I doubt the suicide mission would ever have succeeded (although who knows? She may yet turn on us in ME3!).
3). Perhaps the most sinister point raised would be TIM's long term goals with the reaper base. I can bet keeping the base will mean that a lot of unethical cerberus style experiments will be performed on the base's technology. On top of this cerberus may even gain a lot of power from the base's tech putting them far ahead of any other faction in the galaxy, and perhaps, in the long term securing cerberus's dominance over the galaxy (which is most likely a bad thing unless TIM is replaced by a nicer leader

). My only justification for this is that keeping the base may save many lives from the reapers.
I must agree, it really was a tough decision.