I'm writing a PhD thesis.
Should I use "upcoming" in the following sentence, or is it too informal?
. . . the modifications will be included in the upcoming fourth version of the manual . . .
By upcoming I mean "to be released".
You could omit it altogether.
The salient point is that the modifications will be in the fourth version of the manual. Since your PhD will be published and readable at any date that follows it, including the word 'upcoming' will result in your text becoming out of date.
If it is useful to note that the fourth version has not been released at the time of the publishing of your PhD, a footnote along the lines of "Expected release date: blah blah 2011" might be appropriate.
The dictionary I have does not report upcoming as informal word, nor do I give to the word an informal meaning.
I normally see the word associated to events that are about to happen (e.g., election), but I have also seen the word used in upcoming newsletter.
Instead of upcoming, you could use forthcoming, future, imminent, coming, or impending.