Any transmission swap that uses the original Ford bellhousing should work. This would include a top loader 4-speed, NP435, and there are discusions of using an NV3550 5-speed behind the I6. There probably are a few other options as well. The 60's and 70's (even some of the 80's) fords may have different bellhousing to engine bolt patterns, but the bellhousing to transmission was very common.
Now if you have a late model I6 with the "big bell" that has a V8 bolt pattern, even easier.
One thing that you will have to pay attention to. The length will be longer then with a V8. Since all the swaps are based on the V8, that is what all the measurements are based off of. The I6 is a longer, narrower engine then the V8. This places the bellhousing about 3" further back then a comperable V8. Stock configuration this is taken up with a shorter transmission to transfer case adaptor then what a V8 would use. But since you will be using adaptors based on V8 engines, it will simply move the transfer case back about another 3". Just plan for that seperatly from the typical V8 swap reference material.