I choose Toxic because of the music video. Musical-wise, it's a very tough choice, but Toxic catches my attention immediately while Bad Romance took a while...
I favor Toxic. It stands out in the mainstream pop world as something wholly unique in terms of production. It would be difficult to think of another commercial pop track that pre-dates Toxic from which you could say Toxic was derived. Musically speaking, Toxic is so completely off-trend for songs released in 2003/2004 (music had a decidedly urban sound with dancehall/reggae music also coming to prominence)*that I still find it somewhat shocking it was able to be as successful as it was (at least in the United States). Ultimately, the fact that Toxic was a hit is just a testament to the undeniable quality of the track. You can argue that the electronic presence in pop music was on the rise for years prior to Toxic's release, but you will be hard pressed to find a mainstream electro pop track pre-dating Toxic that's of a similar nature to Toxic, and for what it's worth you aren't likely to find another pop track post-Toxic that can begin to rival the grandness that is Bloodyshy & Avant's stellar production and Britney's captivating performance.
Bad Romance was distinctive in it's own right, and I have always thought it sounds slightly different from Gaga's other hits, but despite the few eccentricities the song has it is still firmly rooted in the foundations of the RedOne sound, which, while novel at one point in time, was certainly well established at the time of Bad Romance's release. The song is amazing, but I think it could have been even more amazing had RedOne's presence not been so identifiable.
"Bad Romance", though I must applause "Toxic" for being unique the way it is, but I still don't see all the appeal.
I still wonder to this very date what would happen if Kylie hadn't turned down such masterpiece that is "Toxic". Homegirl was smoking that good **** without a doubt.
Toxic is such a good single and I think it was the Bad Romance of its time. But Bad Romance is so much more powerful than Toxic. Of course, it's a matter of if you like powerful songs or not so this will definitely come down to preference.