Q:

Longest Text in Latin

What are the longest texts, say top 5, transmitted via manuscript from the Classical/Early Medieval period?

A:

The longest in one package may be
Codex Amiatinus, https://smarthistory.org/codex-amiatinus/  which is the earliest complete text of the Bible.
Isidore of Seville's Etymologies aimed to include all knowledge in one volume. Text 
In monastery Libraries the commonest large multivolume work with most pages was Gregory's Commentary on Job, but this is partly because it was dinnertime reading in big script designed to be read by candle-light.
The longest classical texts change abruptly with the move from the scroll to the codex. Just as there is a jump from manuscript to printed book.
Among the printed books:
Cicero Orationes in 12 Volumes 1642;
Ovid 3 volumes.1682
Augustine Opera 
Before that 
Euclid in fifteen books (translated, I think, by Boethius c.500 Gk to Latin (Lost) and by Adelard of Bath c1100 Arabic to Latin.)
Vergilius Aeneid in six books.
Lucretius DRM in six books.
Livy histories

A:

Cerberus made this valid point:

Can you define length? Number of pages in modern print? In Ancient manuscript? In number of sentences? Words? Letters? I think in words or letters will be quite difficult to compare...

In fact, if we were to merely define length by size, then the longest text would be the Codex Gigas (13th century though), which is the largest manuscript of the Bible ever made (before the printing press) (it also contains other texts though; see article). Here is a picture, just to given a idea of its size:

There are other examples of massive medieval bibles (e.g. here).
Another option to add to the list is Saturnalia, written around 400 AD by somebody called Macrobius. According to this site: 

Although we only have parts of it, this book, written in the 5c A.D., is one of the longest extant works from Late Antiquity.

