1. What ever the leader of your fleet has set
2. Major Upgrades. This is the 3rd one in a holding except for SB in which its the 4th one
3. Dil mine (if not t3)
This holds true if its your fleet or a Beta fleet. The reason I believe Major Upgrades should be done before any other projects is that it opens up other regular projects to be slotted. Also the major upgrades tend to take way more FM's, dil, etc..
When there is a regular project that requires FM's and a Major Upgrade that needs FM's one should usually put the FM's in the Upgrade 1st.
This is just a guideline and not a 'rule'. You should always feel free to donate to whatever project you want to but keep this in mind when donating.