It still depends what you want to achieve whether you are better off using raster or vector data.
If your are using your grid to subdivide an area as an array of containers for geographic features, then stick with vector data. To do this, I would create a polygon grid file and intersect it with each of your data layers. You can then add an ID field that represents the cell's location in the array (and hence it's relative position to a known lat/long coordinate - let's say lower left). Alternatively you can use spatial queries to access your data by selecting a polygon in your vector grid file and then finding all the features in your other file that are contained by it.
OTOH, if you want to do some multi-feature analysis based on presence/abscence then you may be better going down the route of raster analysis. My gut feeling from what you have said is that this is what you are trying to achieve but I am still not 100% sure. You would handle this by creating a set of boolean rasters of a suitable resolution and then performing maths operations on the set (add, subtract, average etc - depending on what questions your are asking).
Let's say you are looking at animal migration. Let's say your model assumes that streams, hedges and towns are all obstacles to migration but roads only reduce the chance of an area being crossed. So you convert your obstacles to a value of '1' and NoData to '0' in each case, except roads where you decide to set the value to 0.5. You can then add all your rasters together in one big stack and predict migration routes.
Ok that's a simplistic example but perhaps you can see why we need EVEN more information on what you are wanting to do.