Siding with the brotherhood and Minutemen and want to make sure there's nothing I can miss or not complete by blowing up the institute.

I haven't cleared the CIT ruins yet and there's lots of quests left to do.

Unfortunately you can't do all quests in one game. Depending on who you side with you'll be locked out of some stuff.

What about collectables? Like bobble heads and magazines.

You can collect all the bobble heads and magazines in one play thought. However, the collectibles can't be transfer to another save game.