I have no idea what you are talking about with MW Tools being updated...as far as I have heard they are not doing squat with it, but if you haven't heard I think they have an update somewhere. I will look for it and let you know. Anyways, any good software of program that does 3rd E D&D should be able to let you update it and refurbish it. If you are in need of a good program, there is a demo of a good program available at www.download.com called DM Genie. It does D&D, D20 Modern and really whatever d20 system game you put into it (if you have time). Again, you can go into the D&D settings and just play around with them and update them, nothing really significant changed in 3.5v so you should be spending too much time (also, it lets you customize your own Campaign).
If your talking about e-tools then go to www.codemonkeypublishing.com . They have taken over and will be fixing all the bugs e-tools had. As for 3.5 I believe they will be selling e-tools 3.5 in the near future.