For the frontend? I run 320x240 15Khz non-interlaced. I think that's the highest, cleanest, most normal res you can go before interlacing assuming you are going with a standard arcade monitor.
Tweaking the games is another story. I've spent many hours setting up the best resolutions and settings for each game. There's a tool on the Ultimarc CD that writes all the ini files for this, but I found that I didn't agree with them entirely. The good news is, once you find a res that works for a game and provides a good aspect ratio without any bastardization (high tech term!), it typically affects 2-10 other games in that same family, maybe more. Just copy the ini contents. And always backup your configs.