A cautionary note...
As a warning against the assumption that present theories are the final word, here are two quotes from The Riddle of the Universe, by Ernst Haeckel, 1899.
‘The existence of ether (or cosmic ether) as a real element is a positive fact, and has been known as such for the last twelve years.’
‘ … all the particular advances in physics and chemistry yield in theoretical importance to the discovery of the great law which brings them to one common focus, the “Law of Substance.” As this fundamental cosmic law established the eternal persistence of matter and force, their unvarying constancy throughout the entire universe…’
And a few years later, Einstein would come and blow it all away! Science, and thus also the Philosophy of Science, should always be open to revise its views and qualify its claims.
For a really substantial anthology, giving a global view of the subject, try Blackwell's Philosophy of Science, edited by Marc Lange. A heavy book (literally) but packed with valuable articles from the last 50 years.
Realism and the character of scientific theories, Scientific Theories and Laws of Nature, natural kinds, causation, probability, metaphysics - the range of issues covered is enormous. But don't always expect an easy read!
For a very well written and clearly presented account of the way in which Philosophy addresses the key issues in science - including the relationship between science and philosophy and issues concerning scientific explanation, theories and models, along with questions of underdeterminism and probability, there is Philosophy of Science by Alex Rosenberg in Routledge's Contemporary Introductions to Philosophy series.
A useful starting point...
for researching Philosophy of Science on the web is: www.trinity.edu/cbrown/science/links.html
which has links to the Stanford Encyclopedia and many other websites.
Controversial when it comes to all matters relating to religion (and inclined to indulge in polemic rather than reason or evidence), I still think that, when it comes to an enthusiastic and brilliant exposition of science, Dawkins is the one to read. Unweaving the Rainbow was the book that, for me, demonstrated his enthusiasm at its best - showing that science need not preclude a sense of wonder at nature.