The Molecule Man's character development can be divided into three eras: before Secret Wars, during Secret Wars, and after Secret Wars.
Before Secret Wars, the Molecule Man was generally a weak-minded and petty villain. Some of his most interesting stories include his first appearance in Fantastic Four 20, his fight with Thing and Man-Thing in Marvel Two-in-One 1, his fight with Iron Man and Man-Thing in Iron Man annual 3, his alliance with Klaw in Fantastic Four 187/188, and his battle against the Avengers in Avengers 215/216, which has some great humor in it.
Secret Wars I transitioned him from a villain to an ex-villain, and his powers greatly increased. He also fell in love with Volcana. It is very recommended.
Secret Wars II was his finest moment. His relationship with Marsha became fully fleshed out, and was written in a very mature way. He had a very well-written relationship with the Beyonder, and ultimately became a hero fighting against the Beyonder. The epilog, in Avengers 266, was excellent. Part of this epilog was retold in Marvel: Eye of the Camera 4, and was also very good. Everything from this era is recommended.
After Secret Wars, his power level changed again in the "Cosmic Cube Retcon" This happened in Fantastic Four 318 and 319.
Since then he appeared in a variety of random issues. Most of these are not particularly noteworthy for their quality or their respect for his character. Fantastic Four annual 27, where he fights Kosmos, is perhaps the best of them.
His most recent appearance was fighting the Dark Avengers (issues 10, 11, and 12), where he was eventually defeated by Sentry (which was a very controversial outcome). Despite the controversy, however, it is a generally good arc.