I noticed absolutely ZERO difference in those games whether it was with or without mods. In fact the open world stutter of Fallout 3 was the sole reason I bought the SSD. I loved that game to hell but I became extremely frustrated with the open world stutter, so I dished out the money for a 256 GB SSD. And to my disappointment there was absolutely Zero difference between it and my 7200 rpm hard drive. I actually measured the frametimes at every point where the stutters occurred, and they were exactly the same. If it was 50 ms on the HDD, it was 50 ms on the SSD. I checked with others on forums, and it was always the same: people who didn't own an SSD claimed "It will make the game butter smooth cause game streams assets" etc, while the people with an actual SSD posted their experience that it provided zero improvement for the stutters.I noticed an immediate benefit when I went to an SSD playing Fallout 3 and New Vegas, though each was with nearly a hundred mods.
The only explanation I have for you noticing an improvement was that you were using a very old 5400 rpm hard drive, maybe in IDE mode, or maybe it was faulty, or fragmented, or maybe you installed it on a drive on the outer track of the disk.