Never owned any Namco game so I cannot state any favourite ones.
I think one problem is that Namco only produced games for the system in its early years and they just withdrew before even developing CD games. Early games (not just Namco ones) on the system were understandably primitive and couldn't use the system to its better potential. Namco's games were usually arcade ports that at first glimpse looked close enough to the arcade originals, but when examined in detail suffered from a lot of sacrifices in nearly every department. That early Hucards were usually small sized didn't help (It was advertised that games could go up to 4 or 8 Mbit right from the beginning, but the truth was early titles couldn't even exceed 2Mbit, which was one reason why R-Type was released in two parts, and this was at a time that even Famicom and SMS titles started to get bigger). They're still good games in their own rights, just not up to the standard of the originals that they're going to emulate.
One example was Dragon Spirit. It looked good and sounded good though a number of stuff were cut, such as the opening cutscene and stages. (I still find this a good conversion, though many people disagree.) The Famicom version looked like a pile of ... er... things but included a lot of original features and cutscenes (even extra ones) to make it enjoyable. This somehow made the PCE version looked barebones in comparison.
Another example was Youkai Douchuuki. The PCE version looked decent, but still, was a scaled down conversion. The Famicom version, however, was greatly expanded even compared to the Arcade version and it looked and sounded great considering the system's limitation.
I think in many cases the developers could try harder, as there were many missed opportunities.
