I'm about to start a new project, and I wanted to get some opinions on the different protein/genetic interaction databases such as IntAct, BioGRID, MINT, etc. What do you guys think of them and are there any advantages/disadvantages to using each one?
Do you want protein or genetic interactions, or both? Some databases focus only on molecular interactions and, strictly speaking, genetic interactions are not molecular interactions.
Protein interactions: If you are interested primary in protein interactions, look first at the IMEx consortium; all of the databases that you mention are a part of it. Their interactions are available through PSICQUIC web services, described here: http://code.google.com/p/psicquic/
Some websites combine data from multiple molecular interaction databases, e.g., Pathway Commons and IRefWeb. I know you can download a combined dataset of interactions from Pathway Commons but I haven't tried doing this with IRefWeb.
Genetic interactions: I think that BioGRID is the only major database that currently curates genetic interactions.
Oooh...have I seen flamewars over this topic! Like all projects, it depends what what you need. But I thought the folks at iRefWeb made a good case for their tool in their paper that I talked about here: Tip of the Week: iRefWeb + protein interaction curation.
Check out both that paper and their site, and the previous paper on the topic that Mike Cusick et al wrote. Those offer some data on the underlying data sets, or ways to think about them at least.
Picking up on Khader's comment and qdjm's response, FlyBase curates Drosophila genetic interactions from the literature (see dump and description), and there are many large-scale PPI datasets generated for this species as well. All of these data are integrated into a nice interface in DroID, The Drosophila Interactions Database, which has it's own viewer and a cytoscape plugin as well. So if you are organism-agnostic and want to explore the effects of different data sources, DroID might be a good resources to check out.