Here are some numbers regarding the time:
methane production in an LV centrifuge is 4 ticks/L at the fastest (foods vary in how much methane they produce, but not how fast, except for foods that output additional items, e.g. golden carrots/apples, which are slower)
biogas production in an LV distillery is 1.25 ticks/L
biogas production in a distillation tower running at minimum voltage is 32 L/tick.
I think biogas has a big advantage in terms of net EU per item - 4 pumpkins is enough to make 1000 mB biomass in an IC2 fluid/solid canning machine (after macerating to bio chaff), which eventually becomes 32000 L biogas in the distillery, or 8000 L biogas per pumpkin, compared to 72 mB methane per potato (or 96 if you use a poisonous potato)
Edit: net EU gains, ignoring transfer losses, and using FTB wiki numbers for gas turbine actual output (which might be based on 5.08 default efficiencies):
poisonous potato = 96 L methane = 3648 EU
processing cost = 1920 EU
net = 1728 EU per poisonous potato, 19 sec = 126 EU/s or 6.3 EU/t with a constant supply of the item
A regular potato nets about 1296 EU.
4 pumpkins = 32000 biogas = 841600 EU fuel value
processing cost:
macerate 16 pumpkin seeds to 1 bio chaff = 800 EU (2 EU/t for 400 ticks)
fluid enrich water with 1 bio chaff = 800 EU (4 EU/t for 200 ticks)
distill 1 L biomass to 32 L biogas 1000 times = 640000 EU
net = 201600 EU per 4 pumpkins, or 50400 per pumpkin (49600 per pumpkin if you use a second macerator to convert the pumpkins to seeds to allow buffering the pumpkins in a chest instead of the seeds)
Edit 2: just for the sake of comparison, here's charcoal to steam via large bronze boiler at 5.08 efficiencies (admittedly automating wood harvesting is impractical without other mods - I've heard about players pulling it off with an imprisoned Wither iirc, but that sounds absurdly dangerous to me - and automating logs to charcoal is mid-game by default in 5.09):
1 charcoal = 16000 L steam (at full heat) / 2 * 0.66 = 5280 EU
wood to charcoal in LV electric furnace = 512 EU (4 EU/t for 128 ticks)
net = 4768 EU per charcoal