One convention I use is to create wrapper classes for all my SFDC SObjects that need some sort of APEX. This way, I can give each SObject custom methods. I also use a Gateway class to collect all related SObjects before executing 1x1 validations/derivations on a trigger list - this avoids too many SOQL call governor issues

Here is a trivial example:

public without sharing class AccountWrapper {

	//	--------------------------------------------------------------------
	//	Wraps the Account object so we can have methods on it 
	//	--------------------------------------------------------------------
	
	//	------------------------------------------------
	//	Properties
	//	------------------------------------------------
	public 	Account					a {get; set;}
	private	Account					aOld;
	private Boolean					isValid		= true;					// passed validation checks?

	
	//	-------------------------------------------
	//	Constructor
	//	-------------------------------------------
	public AccountWrapper(Account a) {
		this.a 		= a;
		this.aOld	= null;
	}
	
	public AccountWrapper(Account a, Account aOld) {
		this.a 		= a;
		this.aOld	= aOld;
	}
	//	---------------------------------------------------------------------
	//	debug 
	//	---------------------------------------------------------------------
	public String debug() {
		return 	'\nName                     : ' + this.a.name  +
			'\nBillingCountry           : ' + this.a.billingCountry
			;
	}
	//	-------------------------------------------
	//	derive:			Field derivations
	//	-------------------------------------------
	public void derive(AccountGateway aGw) {  // AccountGateway is another class where all related records have been collected (Account's Contacts, for example)
		if (!this.isValid) {}
		else {
			// do derivations here
		}
	}	
	
	//	---------------------------------------
	//	prepareForClone:	Get clone source ready - used by VF controller - when overriding clone button 
	//	---------------------------------------	
	public void prepareForClone() {

		
		//	1.	get list of attachments to possibly clone at user's option
		this.attachIdToAttachMap	= new Map<ID,Attachment> ([select id, name, Description 					
											from Attachment where parentId = :this.a.id]);									
		//	2.	Clear fields that can't be cloned 
		
		
	}	
	//	-------------------------------------------
	//	validate:		Does Validations undoable by Force.com Validation Rules; sets instance Vbl isValid
	//	-------------------------------------------
	public void validate(AccountGateway aGw) {
		// do validations here, set this.isValid true or false
		}
	} 


}