I've been both IFB and SBC. Both have their good and their bad.
If I had my preference, I'd be neither. Labels get in the way of too many good people. In Heaven it's not going to matter.:smilewinkgrin:
As for missions, I pastor an SBC deaf church and we support three independent Baptist missionaries to the deaf as well as the IMB. I doubt that there are many IFB churches that do likewise. One of the best (IMHO) IMB missionaries that I know was trained in an IFB college, and there are likely others as well.
Edit: I wanted to add that I did deputation as an IFB missionary and it was the best 18 months of our family's life. We enjoyed our nine years as missionaries with an IFB sending agency and we still enjoy a great relationship with our former IFB sending church and several individuals from churches that formerly supported us.
But when we got to the mission field, we started getting the questionnaires quibbling about which Bible version we used, if we supported women wearing pants, which side if the current split we were on, etc. and etc. and as a result the support dropped (The Lord never let us suffer for it though!). That is the negative side to IFB missions- it is too much like a "beauty contest" and the missionaries have to keep getting "makeovers" in order to keep the support coming in. I know many missionaries that are "this" or "that" when it comes to filling out questionnaires or writing prayer letters but something else entirely in real life. They also tend to speak "evangelistically" a lot- if there aren't any notches in the "Gospel gun" there's usually little support. The pressures to do those things are removed in the SBC program.
All that being said- I thank the Lord for every good Bible-believing, Gospel-preaching, devil-hating, sinner-loving, and disciple-making church and missionary and pray that we will make His savor known in every place.