I am reading up on some of the wars of Tamriel at the moment, I am just wonder which were the biggest ones?
seems War of the Isle in the Second Century of the Third Era was pretty big, but I don't think it was the biggest.

I don't know if this is really an answerable question, but I'm somewhat dissappointed you overlooked the War that started the Third Era itself.

If you meant battles, then there are plenty of them throughout the war I just mentioned.

http://www.imperial-library.info/history/2.shtml

I should really brush up on my lore, but I think the "War of the Red Diamond" ranks rather high on the list, sorry I can't other much more.

The War of Red Diamond raged across most of Tamriel.


-Two emperors/empresses killed: Kyntira II and Uriel III
-Imperial City placed under siege
-Documented fighting in Cyrodiil, Skyrim, Iliac Bay, and Morrowind, with divided allegiances throughout Tamriel
-Six years of fighting to capture Uriel III (son of Potema, wolf queen of Solitude)
-Ten more years to defeat Potema
-Possibly apocryphal (see Jarth's Wolf Queen), but War may have lead to Pelagius III's eventual insanity

Another big war that comes to mind is that between the First Era Reman Empire and Morrowind, which lasted for eighty years--the end of the war is well-documented in 2920.

And of course there are Tiber Septim's conquests: the unification of the Imperial Heartland (Colovian Estates and Nibenay), the fighting in Hammerfell (both initial intervention between the Crowns/Forebears and the successful revolt in Stros M'kai), conquering Valenwood and Summerset Isle with the big stompy robot (which is still going on, according to MK, because the Numidium screws w/time), etc.