I always thought it would've been interesting if B5 got a couple more years. As divinely layered as Season 4 was, both wars could've used more time.
Enterprise should've been given at least another year. Sure, the first two seasons were bland as hell, but the last two were pretty great, especially with Manny Coto at the helm. Had the show started with Season 3, it would probably still be on today.
Other stuff... Firefly, of course, but that's an obvious pick around here. Angel is another one. For more obscure fare, I wish Mission Hill had lasted longer as it was one of the best animated comedies I've ever seen. Clone High also fits into that mold; Duckman slightly less so, but also worth noting.