I use to work at a Honda/Acura dealerships in my past and I came across a grease called Shin-Etsu that works wonders that I want to share with everyone. I purchased my MR2 about 3 years ago and it had the leaky t-tops and wind noise from the door seals. Basically the rubber seals get hard and dry up from the sun/heat and they require to be lubed up. I used this grease to lube up (insert porn music) the seals and wow, leaks and wind noise went away. I lube the seals every 2nd oil change and the seals are nice and soft. On my previous cars I used silicone spray and it was a messy job because you can easily overspray on the glass, dash, etc. And I would not recommend transmission fluid at all as some of the old timers would do.
Now if the rubber seals are too far gone then you will probably have to replace them but I would try this first. Honda or Acura sell this grease and it is around $20 for the tube and it last for quite a while. You do not have to apply a lot of grease, just a little and then massage it into the seal and let it obsorb for about 15 mins. I have used this grease to lube up the seals on my sisters Mazda 626 and the sunroof seals that had moss growing on it, cleaned the seal up and lubed away. Seals look and work great.
Toyota may have a smiliar grease but I am stuck on this stuff. Anyways i hope this helps.