For canon games, I'd have to say that Code Veronica and Nemesis are probably the most underrated. When Code Veronica came out, it was promoted as the true third installment in the series as if to say: Nemesis just never happened, forget that. And still, even to this day Nemesis is overshadowed by the success of Resident Evil 2 and almost never talked/thought about. Then when Code Veronica came out, I think it was so...difficult that it never really caught on but, to be quite honest, I think Code Veronica's difficulty and truly amazing storyline are the reasons I love it. Code Veronica was the perfect way to transition from Raccoon City to another location while still retaining that trapped, hopeless situation feel that, I believe, was lost after the Rockfort Island incident.
For non-canon games, I would have to say Operation Raccoon City and Dead Aim. If Capcom wanted to make Resident Evil a shooting game, Operation Raccoon City was honestly the best way to do it with Dead Aim being a nice stepping stone to get there. Who says you can't having a third person shooter with horror undertones? Not these two titles, that's for sure. Much better than Resident Evil 4 and 5.