I'm sort of looking back at the Starmada Summer of 2011 as a model, but hopefully with a less flexi-fragile system (or a gentleman's agreement that if something is broken, you use it to win once and then can it). I think Full Thrust in one of its several incarnations would probably serve us well, as it is a very simple core game with lots of optional things to experiment with (I for one would be curious to try Colonial Battlefleet's initiative system on top of FT's general mechanics; I'm just not a huge fan of pre-plotted movement). Full Thrust is also old enough and well-enough vetted that its exploitable flaws are known (documented and discussed in the expansion books) and can hopefully be avoided. It also has a nice-looking sample campaign in the back of the FT2E manual.
- Starmada: Nova - we never really gave this one a fair shake, and the seeker rules are pretty neat. On the minus side, forum reports that stacking up weapon traits is still pretty broken.
- Colonial Battlefleet - sort of hampered by lack of good shipyard spreadsheet. I have one half-thrown together, but got bored. Good stealth and initiative rules, and the Raider type from the expansion book looks like fun. On the minus side, fairly heavy bookkeeping for shields.
- Battleshift - Fleet engagements with some cool tactical warp mechanics. If I recall correctly, though, it needs a pretty big playing area, and I've seen roll20 lag out under less.
- Space Hulk. The problem with Space Hulk is that it's unusually stressful, because there is some serious "oh god oh god we're all going to die" going on continuously (... holy cow, this must be what it's like to play in my ACKS games. No wonder they keep disintegrating! On the other hand, if you play ACKS well, it's less of a problem than if you play Space Hulk well, because the DM is slightly less actively malicious than the 'stealer player). Also the maps are deceptively expansive.
- BattleTech Lite - light to medium mechs from the earliest time period only, and perhaps no melee. Could be fun as long as you keep the total number of armor / structure points low.
- Domains at War: Battles - Our experiences so far suggest that DaW:B is too heavy unless there's some significant investment in the outcome (ie, a PC realm at stake). On the other hand, two games between inexperienced players is not a whole lot to go by. I've been meaning to write some scenarios for this - the system could definitely use one highlighting the fortification rules, and everybody loves Helm's Deep.
- Hell, a sample DaW:C campaign would be fun too, and if the battles were resolved using the Campaigns rules, it might work alright for one-off afternoon games (though I sort of expect a lot of overhead from the recon rules - TODO automate recon). I could steal something from Crusader Kings and keep the magic-and-wyvern-cavalry level historically low for ease of use.
- Anything in the 15-25mm infantry sphere - I have my doubts about how well roll20 would handle these, and Vassal suffers from limited plugins. Options include Stargrunt, Gruntz, WH40k, and many many others.
- Dirtside or other 6mm microarmor games - Again, I don't think this one would do well on roll20. Also chit-based damage.