Functionally there is little difference between the muskets used by the assorted belligerents during the Napoleonic Wars. All standard issue muskets of the era were smoothbore flintlock muskets. The only real differences are essentially cosmetic; ie iron vs brass fittings and barrel bands vs pins/keys. Other than that, differences include the established bore sizes used by each nation, approximately .69 to .75 caliber.

That leaves us with manufacturing techniques and length of service to judge the relative quality of the muskets used:
Since the Prussians adopted a new musket in 1809 their M1740 shouldn't be considered for a spot as a top contender. The Model 1809 wasn't replaced until 1839.
Likewise, the Russians adopted a new model in 1808 the supplanted the Model 1798 and 1805 Muskets. A replacement for the Model 1808 wasn't adopted until 1828.
The Austrians started out with the Model 1798, which was improved some in 1807, but not redesigned and replaced until the adoption of the Model 1828.
The English utilized the 3rd Land India Pattern Musket throughout the era and did not adopt a replacement for it until 1839. The India Pattern musket was adopted in 1798 and saw a minor change in the hammer design in 1809.
The French would have fought with mostly Mle 1777 and Year IX (1800) Muskets. A new design was adopted in 1816 and quickly replaced in 1822.

Based on the adoption of new muskets it would seem that the British had most confidence in their arms, since they didn't design a full replacement for 24 years after Waterloo.
French arms of the era were of good quality, and though replaced by more modern designs in short order, the changes were not very substantive and were mostly focused on improving the manufacturing process.
IMHO, the Prussian Model 1809 Musket is a quality arm. Though fairly limited numbers of them were produced in time to be used during the Napoleonic Wars, they would continue to serve until being replaced with in 1839 with a new model that is for all practical purposes, a percussion version of the M1809.
There is little English language information on Russian arms of the 19th century. Most of what does exist focuses on the Crimean War, but it is critical of the quality and serviceability of their muskets. Though the serviceability issues could be explained by the Russian serf soldier of the period.
I am not familiar enough with Austrian arms of the period to weigh in much in regards to their quality, but later 19th century Austrian arms are generally quite well made. The k.k. Army obviously saw a need to develop a new infantry musket at the end of the conflicts, but that may have been influenced more by their lack of battlefield success than real issues with the muskets then in service.

There is not much difference in the arms of say 1810 and the arms of 1780. The major improvements made to military arms of the interwar era would have been focused on improving standardization of guns; an issue not solved by most European countries until the 1850s or 1860s. Due to the massive number of arms required during the Napoleonic wars a number of nations simplified their muskets to more easily produce them, or made minor improvements to better their field service; eg the Austrian M1798 and the British Brown Bess.

The arms used during the English Civil War, though still large bore smoothbore muskets, are vastly different from the weapons used in the mid 18th and early 19th centuries. For starters the muskets of the English Civil War would have been predominately matchlock weapons that took plug rather than conventional socket bayonets. George Moller's "American Military Shoulder Arms Volume I" can provide some excellent insight on the differences.