Is there a version of R Yaakov Emdens siddur online? Also how is the Siddur different from the Artscroll Ashkenazi Siddur which I am more familiar with?
The book is in Hebrew Books
R' Yaakov Emden's original siddur (which the one in kouty's answer is based on, although with a lot of changes and interpolations, hence Joshua Pearl's comment there) is on Hebrewbooks here (weekday and Shabbos davening), here (Rosh Chodesh and the yearly cycle) and here (lifecycle). Its main feature is his extensive commentary, including many different facets: notes on grammar, pshat, halachah, Kabbalah, etc. (Eshkol reprinted it some years ago, and included also more commentary of his found in manuscript.)
The nusach is basically standard Ashkenaz, although there are some places where R' Yaakov adds things that aren't part of the standard nusach (such as the detailed descriptions of the korbanos), or has a nonstandard vocalization (for example, he has the reish of רבי with a sheva, instead of earlier Ashkenazic (and unchanged Sephardic) chirik.